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
http://creativecommons.org/licenses/by/4.0/
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 OWL specification label
BFO OWL specification label
BFO OWL规范标签
BFO OWL规范标签
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
Person:Alan Ruttenberg
Really of interest to developers only
只对开发人员感兴趣
BFO CLIF specification label
BFO CLIF specification label
BFO CLIF规范标签
BFO CLIF规范标签
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.
表示细胞系的LINCS ID的注释属性。
Oliver He, Jiangan Xie
Oliver He, Jiangan Xie
Oliver He, Jiangan Xie, Jie Zheng
Cell line LINCS ID
LINCS ID
细胞系LINCS ID
细胞系LINCS ID
editor preferred label
editor preferred label
editor preferred term
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
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
editor preferred label
editor preferred label
editor preferred term
editor preferred term
editor preferred term~editor preferred label
editor preferred term~editor preferred label
编辑首选术语
编辑首选术语
编辑首选术语~编辑首选标签
编辑首选标签
编辑首选标签
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
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
IAO:0000112
uberon
example_of_usage
true
example_of_usage
example of usage
example of usage
用法示例
用法示例
has curation status
有管理状态
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
OBI_0000281
has curation status
has curation status
有管理状态
有管理状态
definition
definition
textual 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.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition
definition
textual definition
textual definition
定义
定义
文本定义
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。
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
IAO:0000116
IAO:0000116
uberon
uberon
editor_note
editor_note
编辑_注释
true
editor_note
editor_note
编辑_注释
IAO:0000116
IAO:0000116
uberon
uberon
editor_note
editor_note
1
true
editor_note
editor_note
editor note
editor note
编者注
编者注
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。
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition editor
definition editor
term editor
term editor
术语编辑者
术语编辑者
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)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
alternative term
alternative term
替代术语
替代术语
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.
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
PERSON:Daniel Schober
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
论OBO-讨论邮件-列表,请参阅http://bit.ly/hgm99w
definition source
definition source
定义来源
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.
url:http://purl.obolibrary.org/obo/iao.owl
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.
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
has obsolescence reason
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
PERSON:Alan Ruttenberg
IAO:0000232
IAO:0000232
uberon
uberon
curator_notes
curator_notes
管理者_注释
true
curator_notes
curator_notes
管理者_注释
IAO:0000232
uberon
curator_notes
1
true
curator_notes
curator note
curator note
curator notes
curator notes
管理者注释
管理者注释
term tracker item
the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
An IRI or similar locator for a request or discussion of an ontology term.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'tracker item' can associate a tracker with a specific ontology term.
term tracker item
The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
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
Chris Mungall
expand expression to
expand expression to
OBO foundry unique label
An alternative name for a class or property which is unique across the OBO Foundry.
The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
PERSON:Alan Ruttenberg
PERSON:Bjoern Peters
PERSON:Chris Mungall
PERSON:Melanie Courtot
GROUP:OBO Foundry <http://obofoundry.org/>
OBO foundry unique label
elucidation
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
elucidation
elucidation
说明
说明
has associated axiom(nl)
具有相关联的公理(nl)
Person:Alan Ruttenberg
Person:Alan Ruttenberg
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(nl)
has associated axiom(nl)
具有相关联的公理(nl)
具有相关联的公理(nl)
has associated axiom(fol)
具有相关联的公理(fol)
Person:Alan Ruttenberg
Person:Alan Ruttenberg
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 associated axiom(fol)
has associated axiom(fol)
具有相关联的公理(fol)
具有相关联的公理(fol)
has axiom id
Person:Alan Ruttenberg
Person:Alan Ruttenberg
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
axiom id
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
Person:Alan Ruttenberg
Person:Alan Ruttenberg
term replaced by
term replaced by
an annotation property that lists keyword(s) useful for literature tagging and retrieval of sentences containing the type (or kind) of entity (e.g., interaction) as shown by the ontology term label and definition.
Yongqun He
has literature mining keywords
the symbol assigned by the nomenclature authority
Oliver He, Yue Liu
symbol from nomenclature authority
the full name assigned by the nomenclature authority
Oliver He, Yue Liu
full name from nomenclature authority
A GeneID in the NCBI Gene database
Oliver He, Yue Liu
NCBI GeneID
the NCBI LocusTag name of a gene
Oliver He, Yue Liu
NCBI LocusTag
the map location of a gene
Oliver He, Yue Liu
gene map location
a date of content modification
Oliver He, Yue Liu
modification date
The NCBITaxon ontology ID of an organism.
Oliver He, Yue Liu
organism NCBITaxon ID
A chromosome ID where a gene is located.
Oliver He
chromosome ID of gene
an annotation property that specifies the type of a gene
Oliver He
type of gene
an annotation property that specifies a nomenclature status
Oliver He
nomenclature status
an annotation property that shows the GO information associated with a specific gene.
Yongqun He
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).
Yongqun He
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/).
Edison Ong; Yongqun He; Yu Lin
has Victors annotation
The idenfier of the entity stored in the Victors database (http://www.phidias.us/victors/).
Edison Ong; Yongqun He; Yu Lin
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
https://code.google.com/p/obo-relations/wiki/ROAndTime
https://github.com/oborel/obo-relations/wiki/ROAndTime
S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
https://orcid.org/0000-0002-6601-2165
RO:0002174
uberon
dubious_for_taxon
true
true
dubious_for_taxon
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
dubious_for_taxon
S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
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
https://orcid.org/0000-0002-6601-2165
RO:0002175
applicable for taxon
uberon
present_in_taxon
true
true
present_in_taxon
present in taxon
present_in_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
defined by inverse
Used to annotate object properties to describe a logical meta-property or characteristic of the object property.
logical macro assertion on an object property
logical macro assertion on an annotation property
relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y
The general property hierarchy is:
"directly P" SubPropertyOf "P"
Transitive(P)
Where we have an annotation assertion
"directly P" "is direct form of" "P"
If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'
Chris Mungall
is direct form of
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
is a defining property chain axiom
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
cjm
2018-03-14T00:03:16Z
is positive form of
cjm
2018-03-14T00:03:24Z
is negative form of
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.
cjm
2018-10-21T19:46:34Z
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.
is homeomorphic for
An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class.
UBPROP:0000001
uberon
external_definition
true
external_definition
This annotation property may be replaced with an annotation property from an external ontology such as IAO
external_definition
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.
A textual description of an axiom loss in this ontology compared to an external ontology.
UBPROP:0000002
uberon
axiom_lost_from_external_ontology
true
axiom_lost_from_external_ontology
This annotation property may be replaced with an annotation property from an external ontology such as IAO
axiom_lost_from_external_ontology
A textual description of an axiom loss in this ontology compared to an external ontology.
Notes on the homology status of this class.
UBPROP:0000003
uberon
homology_notes
true
homology_notes
This annotation property may be replaced with an annotation property from an external ontology such as IAO
homology_notes
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.
UBPROP:0000005
uberon
external_comment
true
external_comment
This annotation property may be replaced with an annotation property from an external ontology such as IAO
external_comment
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.
UBPROP:0000006
uberon
implements_design_pattern
true
implements_design_pattern
implements_design_pattern
Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'.
UBPROP:0000007
uberon
has_relational_adjective
true
has_relational_adjective
has_relational_adjective
Notes on the how instances of this class vary across species.
UBPROP:0000008
uberon
taxon_notes
true
taxon_notes
taxon_notes
Notes on the how instances of this class vary across species.
Notes on the evolved function of instances of this class.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
UBPROP:0000009
uberon
function_notes
true
function_notes
function_notes
Notes on the evolved function of instances of this class.
Notes on the structure, composition or histology of instances of this class.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
UBPROP:0000010
uberon
structure_notes
true
structure_notes
structure_notes
Notes on the structure, composition or histology of instances of this class.
Notes on the ontogenic development of instances of this class.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
UBPROP:0000011
uberon
development_notes
true
development_notes
development_notes
Notes on the ontogenic development of instances of this class.
Notes on how similar or equivalent classes are represented in other ontologies.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
UBPROP:0000012
uberon
external_ontology_notes
true
external_ontology_notes
external_ontology_notes
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.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
UBPROP:0000013
uberon
terminology_notes
true
terminology_notes
terminology_notes
Notes on how lexical conventions regarding this class, in particular any issues that may arise due to homonyny or synonymy.
UBPROP:0000100
uberon
is_count_of
true
is_count_of
is count of
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)
UBPROP:0000101
uberon
preceding_element_is
true
preceding_element_is
preceding element is
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.
UBPROP:0000103
uberon
pharyngeal_arch_number
true
pharyngeal_arch_number
pharyngeal arch number
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.
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
UBPROP:0000202
uberon
fma_set_term
true
fma_set_term
fma_set_term
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
FMA
IUPAC NAME
Manually annotated by ChEBI Team
DO_AGR_slim
DO_FlyBase_slim
DO_MGI_slim
DO_cancer_slim
DO_rare_slim
NCIthesaurus
TopNodes_DOcancerslim
Term not to be used for direct annotation
Term not to be used for direct manual annotation
AGR slim
Aspergillus GO slim
Candida GO slim
ChEMBL protein targets summary
FlyBase Drosophila GO ribbon slim
Generic GO slim
Metagenomics GO slim
Mouse GO slim
PIR GO slim
Plant GO slim
Fission yeast GO slim
Yeast GO slim
A metadata relation between a class and its taxonomic rank (eg species, family)
ncbi_taxonomy
has_rank
Label appended to organism-specific terms in place of scientific name
Unique short label for PRO terms for display purposes; based on orthology
eco subset
abbreviation
A historic synonym, no longer encouraged
dubious or contested synonym
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
latin term
expert consultation and attribution required
plural term
taxonomic disambiguation
CUMBO
developmental_classification
A class that represents an early developmental structure, like a blastocyst. This part of the ontology is undergoing review to remove inappropriate grouping classes.
EFO slim
derived from the union of EHDAA2 and EMAPA - still to be checked
functional_classification
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
Phenotype slim
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.
uberon
dc-contributor
true
dc-contributor
An entity responsible for making contributions to the
content of the resource.
Contributor
Contributor
contributor
Examples of a Creator include a person, an organisation,
or a service. Typically, the name of a Creator should
be used to indicate the entity.
uberon
dc-creator
true
dc-creator
An entity primarily responsible for making the content
of the resource.
Creator
Creator
creator
Typically, Date will be associated with the creation or
availability of the resource. Recommended best practice
for encoding the date value is defined in a profile of
ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format.
A date associated with an event in the life cycle of the
resource.
Date
Date
dc: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.
uberon
dc-description
true
dc-description
An account of the content of the resource.
Description
Description
description
Typically, Format may include the media-type or dimensions of
the resource. Format may be used to determine the software,
hardware or other equipment needed to display or operate the
resource. Examples of dimensions include size and duration.
Recommended best practice is to select a value from a
controlled vocabulary (for example, the list of Internet Media
Types [MIME] defining computer media formats).
The physical or digital manifestation of the resource.
Format
Format
The present resource may be derived from the Source resource
in whole or in part. Recommended best practice is to reference
the resource by means of a string or number conforming to a
formal identification system.
uberon
dc-source
true
dc-source
A reference to a resource from which the present resource
is derived.
Source
Source
derived from resource
Typically, a Subject will be expressed as keywords,
key phrases or classification codes that describe a topic
of the resource. Recommended best practice is to select
a value from a controlled vocabulary or formal
classification scheme.
The topic of the content of the resource.
Subject and Keywords
Subject and Keywords
Typically, a Title will be a name by which the resource is
formally known.
uberon
dc-title
true
dc-title
A name given to the resource.
Title
Title
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
Resource Type
Mark Miller
2018-05-11T13:47:29Z
license
created_by
creation_date
has_alternative_id
has_broad_synonym
database_cross_reference
database_cross_reference
数据库_交叉_引用
数据库_交叉_引用
has_exact_synonym
has_narrow_synonym
disease_ontology
has_obo_namespace
has_obo_namespace
有_obo_命名空间
有_obo_命名空间
has_related_synonym
has_scope
has_synonym_type
id
in_subset
shorthand
shorthand
is defined by
is defined by
This is an experimental annotation
label
label
label
标签
uberon
foaf-homepage
true
foaf-homepage
homepage
uberon
foaf-page
true
foaf-page
page
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
BFO:0000050
external
protein
uberon
part_of
part_of
part of
part of
part_of
part_of
http://www.obofoundry.org/ro/#OBO_REL:part_of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)
A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
BFO:0000051
chebi_ontology
external
protein
uberon
has_part
false
has_part
has part
has part
has_part
inheres-in_at
inheresInAt
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 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])
(iff (inheresInAt a b t) (and (DependentContinuant a) (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))) // axiom label in BFO2 CLIF: [051-002]
bearer-of_st
bearerOfAt
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)
BFO2 Reference: independent continuant that is not a spatial region
BFO2 Reference: specifically dependent continuant
(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
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])
(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]
realized-in
realizedIn
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])
[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
realized in
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]
realizes
realizes
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
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])
(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]
participates-in_st
participatesInAt
[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])
BFO:0000056
uberon
participates_in
participates_in
participates in
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
http://www.obofoundry.org/ro/#OBO_REL:preceded_by
BFO:0000062
is preceded by
takes place after
uberon
preceded_by
preceded_by
preceded by
preceded_by
is preceded by
SIO:000249
takes place after
Allen:precedes
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.
BFO:0000063
uberon
precedes
precedes
precedes
precedes
occurs-in
occursIn
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
BFO:0000066
external
occurs_in
occurs_in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
occurs in
occurs in
contains-process
containsProcess
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
BFO:0000067
uberon
contains_process
contains_process
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
contains process
s-depends-on_at
specificallyDependsOn
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
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]
f-of_at
functionOfAt
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
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])
(iff (functionOf a b t) (and (Function a) (inheresInAt a b t))) // axiom label in BFO2 CLIF: [067-001]
q-of_at
qualityOfAt
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
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])
(iff (qualityOfAt a b t) (and (Quality a) (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))) // axiom label in BFO2 CLIF: [056-002]
r-of_at
roleOfAt
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
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])
(iff (roleOfAt a b t) (and (Role a) (inheresInAt a b t))) // axiom label in BFO2 CLIF: [065-001]
located-in_at
locatedInAt
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)'.
BFO2 Reference: independent continuant
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
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])
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-at-r_st
occupiesSpatialRegionAt
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)
BFO2 Reference: independent continuant
BFO2 Reference: spatial region
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
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]
has-f_st
hasFunctionAt
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
a has_function b at t =Def. b function_of a at t. (axiom label in BFO2 Reference: [070-001])
(iff (hasFunctionAt a b t) (functionOf b a t)) // axiom label in BFO2 CLIF: [070-001]
has-q_st
has quality at some time
has-r_st
hasRoleAt
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
a has_role b at t =Def. b role_of a at t. (axiom label in BFO2 Reference: [068-001])
(iff (hasRoleAt a b t) (roleOfAt b a t)) // axiom label in BFO2 CLIF: [068-001]
has-g-dep_st
[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
d-of_at
dispositionOfAt
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
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])
(iff (dispositionOf a b t) (and (Disposition a) (inheresInAt a b t))) // axiom label in BFO2 CLIF: [066-001]
exists-at
existsAt
BFO2 Reference: entity
BFO2 Reference: temporal region
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
b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002])
has-d_st
hasDispositionAt
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
a has_disposition b at t =Def. b disposition_of a at t. (axiom label in BFO2 Reference: [069-001])
(iff (hasDispositionAt a b t) (dispositionOf b a t)) // axiom label in BFO2 CLIF: [069-001]
has-material-basis_at
hasMaterialBasisAt
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
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]
o-has-part
hasOccurrentPart
[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
b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
(iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001]
o-has-ppart
hasProperOccurrentPart
[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
has profile
has-t-part
[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
r-location-of_st
[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
has-s-dep_st
[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
occupied-by
[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_st
material basis of at some time
member-part-of_st
memberPartOfAt
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)
BFO2 Reference: object
BFO2 Reference: object aggregate
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
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])
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]
occupies
occupiesSpatiotemporalRegion
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
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])
o-part-of
occurrentPartOf
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.
BFO2 Reference: 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])
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
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]
profile-of
processProfileOf
process profile of
t-ppart-of
properTemporalPartOf
proper temporal part of
c-ppart-of_at
properContinuantPartOfAt
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
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])
(iff (properContinuantPartOfAt a b t) (and (continuantPartOfAt a b t) (not (= a b)))) // axiom label in BFO2 CLIF: [004-001]
o-ppart-of
properOccurrentPartOf
[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
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]
t-part-of
temporalPartOf
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
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]
st-projects-onto-s_st
projects onto spatial region at some time
s-projection-of-st_st
spatial projection of spatiotemporal at some time
st-projects-onto-t
projects onto temporal region
t-projection-of-st
temporal projection of spatiotemporal
spans
occupiesTemporalRegion
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
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])
span-of
spanOf
[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
during-which-exists
[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
bearer-of_at
bearerOfAt
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 all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'bearer of@en(x,y,t)'.
BFO2 Reference: independent continuant that is not a spatial region
BFO2 Reference: specifically dependent continuant
(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 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])
(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]
has-q_at
has quality at all times
has-f_at
hasFunctionAt
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 all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and '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 all times
a has_function b at t =Def. b function_of a at t. (axiom label in BFO2 Reference: [070-001])
(iff (hasFunctionAt a b t) (functionOf b a t)) // axiom label in BFO2 CLIF: [070-001]
has-r_at
hasRoleAt
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 all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and '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 all times
a has_role b at t =Def. b role_of a at t. (axiom label in BFO2 Reference: [068-001])
(iff (hasRoleAt a b t) (roleOfAt b a t)) // axiom label in BFO2 CLIF: [068-001]
has-d_at
hasDispositionAt
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 all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and '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 all times
a has_disposition b at t =Def. b disposition_of a at t. (axiom label in BFO2 Reference: [069-001])
(iff (hasDispositionAt a b t) (dispositionOf b a t)) // axiom label in BFO2 CLIF: [069-001]
material-basis-of_at
material basis of at all times
participates-in_at
participatesInAt
participates in at all times
has-s-dep_at
has specific dependent at all times
s-depends-on_st
specificallyDependsOn
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 some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & '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 some time
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]
located-in_st
locatedInAt
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 some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'located in@en'(x,y,t)
BFO2 Reference: independent continuant
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 some time
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])
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]
member-part-of_at
memberPartOfAt
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 all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'member part of@en(x,y,t)'.
BFO2 Reference: object
BFO2 Reference: object aggregate
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 all times
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])
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]
c-ppart-of_st
properContinuantPartOfAt
[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
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 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)
(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 some time
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])
(iff (properContinuantPartOfAt a b t) (and (continuantPartOfAt a b t) (not (= a b)))) // axiom label in BFO2 CLIF: [004-001]
c-part-of_st
continuantPartOfAt
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])
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.
BFO2 Reference: continuant
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
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])
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]
c-part-of_at
continuantPartOfAt
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 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)'.
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])
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.
BFO2 Reference: continuant
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 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'
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 all times
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])
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]
has-t-ppart
has proper temporal part
history-of
historyOf
[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
has-history
hasHistory
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
c-part-of-object_at
[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
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'
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
cjm
2009-07-31T02:15:46Z
BSPO:0000096
uberon
anterior_to
anterior_to
anterior_to
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).
BSPO:0000097
uberon
distal_to
distal_to
distal_to
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).
BSPO:0000098
uberon
dorsal_to
dorsal_to
dorsal_to
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.
BSPO:0000099
caudal_to
uberon
posterior_to
posterior_to
posterior_to
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.
BSPO:0000100
uberon
proximal_to
proximal_to
proximal_to
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).
BSPO:0000102
uberon
ventral_to
ventral_to
ventral_to
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.
BSPO:0000107
uberon
deep_to
deep_to
deep_to
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.
BSPO:0000108
uberon
superficial_to
superficial_to
superficial_to
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.
BSPO:0000120
uberon
in_left_side_of
in_left_side_of
in_left_side_of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion.
BSPO:PATO_mtg_2009
X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion.
BSPO:0000121
uberon
in_right_side_of
in_right_side_of
in_right_side_of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion.
BSPO:PATO_mtg_2009
X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion.
BSPO:0000122
uberon
in_posterior_side_of
in_posterior_side_of
in_posterior_side_of
X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion.
BSPO:PATO_mtg_2009
X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion.
BSPO:0000123
uberon
in_anterior_side_of
in_anterior_side_of
in_anterior_side_of
X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion.
BSPO:PATO_mtg_2009
X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.
BSPO:0000124
uberon
in_proximal_side_of
in_proximal_side_of
in_proximal_side_of
X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.
BSPO:PATO_mtg_2009
X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion.
BSPO:0000125
uberon
in_distal_side_of
in_distal_side_of
in_distal_side_of
X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion.
BSPO:PATO_mtg_2009
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
BSPO:0000126
uberon
in_lateral_side_of
in_lateral_side_of
in_lateral_side_of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
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
BSPO:0001106
uberon
proximalmost_part_of
proximalmost_part_of
proximalmost_part_of
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.
BSPO:0001107
uberon
immediately_deep_to
immediately_deep_to
immediately_deep_to
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
BSPO:0001108
uberon
distalmost_part_of
distalmost_part_of
distalmost_part_of
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.
person:Alan Ruttenberg
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
person:Alan Ruttenberg
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
has material basis in
has_material_basis_in
is_specified_input_of
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
Alan Ruttenberg
PERSON:Bjoern Peters
is_specified_input_of
is_specified_output_of
is_specified_output_of
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
Alan Ruttenberg
PERSON:Bjoern Peters
is_specified_output_of
achieves_planned_objective
A cell sorting process achieves the objective specification 'material separation objective'
This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
BP, AR, PPPB branch
PPPB branch derived
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
achieves_planned_objective
has grain
the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form
PERSON: Alan Ruttenberg
PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
has grain
objective_achieved_by
This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
OBI
OBI
objective_achieved_by
a 'part of continuant at some time' relation that incides a genome belongs to a organism.
Yongqun He, Bin Zhao
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.
Oliver He, Yue Liu
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.
Edison Ong; Yongqun He; Yu Lin
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.
Edison Ong; Yongqun He
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.
Edison Ong; Yongqun He
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.
Edison Ong; Yongqun He; Yu Lin
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.
Edison Ong; Yongqun He; Yu Lin
gene mutant attenuated in host
Edison Ong; Yongqun He; Yu Lin
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.
Edison Ong; Yongqun He
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.
Edison Ong; Yongqun He
has HPI pathogen
Edison Ong; Yongqun He
has HPI host organism
Edison Ong; Yongqun He
has HPI host cell
Edison Ong; Yongqun He
has HPI host cell line cell
Edison Ong
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
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
RO:0000053
uberon
bearer_of
bearer_of
bearer of
bearer of
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
RO:0000056
protein
participates_in
false
participates_in
participates in
participates_in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
http://www.obofoundry.org/ro/#OBO_REL:has_participant
has participant
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
is concretized as
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
concretizes
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
function_of
is function of
function of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
has function
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
inverse of has disposition
disposition of
derives from
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
derives_from
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.
RO:0001000
protein
derives_from
derives_from
derives from
derives_from
derives_from
this parent cell derives into this cell (cell division)
this parent nucleus derives into this nucleus (nuclear division)
a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
derives_into
derives into
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
RO:0001015
uberon
location_of
location_of
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
contained in
contains
RO:0001019
uberon
contains
contains
contains
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
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
located_in
http://www.obofoundry.org/ro/#OBO_REL:located_in
RO:0001025
protein
uberon
located_in
located_in
located in
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.
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
RO:0002000
uberon
boundary_of
boundary_of
2D boundary of
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
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.
David Osumi-Sutherland
has boundary
has_2D_boundary
RO:0002002
uberon
has_boundary
has_boundary
has 2D boundary
has boundary
David Osumi-Sutherland
http://www.ncbi.nlm.nih.gov/pubmed/22402613
RO:0002005
nerve supply
uberon
innervated_by
innervated_by
http://code.google.com/p/obo-relations/issues/detail?id=6
innervated_by
innervated_by
nerve supply
FMA:85999
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
David Osumi-Sutherland
RO:0002007
uberon
bounding_layer_of
bounding_layer_of
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.
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
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.
dos
2017-05-24T09:30:46Z
has regulatory component activity
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.
dos
2017-05-24T09:31:01Z
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.
dos
2017-05-24T09:31:17Z
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
dos
2017-05-24T09:44:33Z
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
has component activity
w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
dos
2017-05-24T09:49:21Z
has component process
A 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.
dos
2017-07-19T17:30:36Z
has ligand
dos
2017-09-17T13:52:24Z
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.
directly regulated by
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.
GOC:dos
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.
dos
2017-09-17T13:52:38Z
directly negatively regulated by
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.
GOC:dos
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.
dos
2017-09-17T13:52:47Z
directly positively regulated by
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.
GOC:dos
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
dos
2017-09-22T14:14:36Z
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
has effector activity
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.
GOC:dos
David Osumi-Sutherland
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)
David Osumi-Sutherland
starts_at_end_of
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].
RO:0002087
directly preceded by
is directly preceded by
is immediately preceded by
starts_at_end_of
uberon
immediately_preceded_by
immediately_preceded_by
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
immediately_preceded_by
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].
SIO:000251
is immediately preceded by
SIO:000251
David Osumi-Sutherland
ends_at_start_of
meets
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
BFO_0000051 some (BFO_0000050 some ?Y)
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
RO:0002131
uberon
overlaps
overlaps
overlaps
overlaps
true
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?)))
RO:0002134
uberon
innervates
innervates
http://code.google.com/p/obo-relations/issues/detail?id=6
innervates
innervates
X continuous_with Y if and only if X and Y share a fiat boundary.
David Osumi-Sutherland
connected to
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)
RO:0002150
uberon
continuous_with
continuous_with
continuous with
continuous_with
FMA:85972
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
BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
spatially disjoint from
https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern
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
RO:0002170
uberon
connected_to
connected_to
Connection does not imply overlaps.
connected to
connected to
https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern
https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern
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.
The M8 connects Glasgow and Edinburgh
a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
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)
RO:0002176
uberon
connects
connects
connects
connects
https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern
https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern
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.
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)
RO:0002177
uberon
attaches_to_part_of
attaches_to_part_of
attached to part of
attaches_to_part_of
true
true
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
RO:0002178
arterial supply of
uberon
supplies
supplies
source: FMA
supplies
supplies
arterial supply of
FMA:86003
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
RO:0002179
drains blood from
drains from
uberon
drains
drains
source: Wikipedia
drains
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.
RO:0002180
protein
uberon
has_component
false
has_component
has component
has component
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
Chris Mungall
David Osumi-Sutherland
Melissa Haendel
Terry Meehan
RO:0002202
uberon
develops_from
develops_from
This is the transitive form of the develops from relation
develops from
develops_from
inverse of develops from
Chris Mungall
David Osumi-Sutherland
Terry Meehan
RO:0002203
uberon
develops_into
develops_into
develops into
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.
Chris Mungall
David Osumi-Sutherland
has developmental precursor
FBbt
RO:0002207
uberon
directly_develops_from
directly_develops_from
TODO - add child relations from DOS
directly develops from
directly_develops_from
inverse of directly develops from
developmental precursor of
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
Chris Mungall
David Hill
Tanya Berardini
GO
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates (processual)
false
RO:0002211
external
regulates
regulates
regulates
regulates
Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
Chris Mungall
negatively regulates (process to process)
RO:0002212
external
negatively_regulates
negatively_regulates
negatively regulates
negatively regulates
Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
Chris Mungall
positively regulates (process to process)
RO:0002213
external
positively_regulates
positively_regulates
positively regulates
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.
Chris Mungall
has function realized in
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)".
RO_0000053 some (RO_0000054 only ?Y)
RO:0002215
protein
uberon
capable_of
false
capable_of
capable of
capable of
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.
Chris Mungall
has function in
RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))
RO:0002216
uberon
capable_of_part_of
capable_of_part_of
capable of part of
capable of part of
true
x actively participates in y if and only if x participates in y and x realizes some active role
Chris Mungall
agent in
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
Chris Mungall
has agent
obsolete has active participant
true
surrounded by
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
Chris Mungall
RO:0002219
uberon
surrounded_by
surrounded_by
surrounded by
surrounded_by
x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y
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
Chris Mungall
RO:0002220
uberon
adjacent_to
adjacent_to
adjacent to
adjacent to
adjacent_to
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.
inverse of surrounded by
inverse of surrounded_by
Chris Mungall
RO:0002221
uberon
surrounds
surrounds
surrounds
surrounds
inverse of surrounded_by
move to BFO?
Chris Mungall
Allen
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporal relation
temporally related to
Relation between occurrents, shares a start boundary with.
inverse of starts with
Chris Mungall
Allen
RO:0002223
uberon
starts
starts
starts
starts
Relation between occurrents, shares a start boundary with.
Allen:starts
Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
Chris Mungall
started by
RO:0002224
uberon
starts_with
starts_with
starts with
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
Chris Mungall
RO:0002225
uberon
develops_from_part_of
develops_from_part_of
develops from part of
develops_from_part_of
x develops_in y if x is located in y whilst x is developing
Chris Mungall
EHDAA2
Jonathan Bard, EHDAA2
RO:0002226
uberon
develops_in
develops_in
This relation take from EHDAA2 - precise semantics yet to be defined
develops in
develops_in
Relation between occurrents, shares an end boundary with.
inverse of ends with
Chris Mungall
RO:0002229
finishes
uberon
ends
ends
ends
ends
Relation between occurrents, shares an end boundary with.
Allen:starts
ZFS:finishes
x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
Chris Mungall
finished by
RO:0002230
uberon
ends_with
ends_with
ends with
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
Chris Mungall
starts with process that occurs in
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
Chris Mungall
ends with process that occurs in
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.
Chris Mungall
consumes
has input
p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
Chris Mungall
produces
has output
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
Chris Mungall
RO:0002254
uberon
has_developmental_contribution_from
has_developmental_contribution_from
has developmental contribution from
has developmental contribution from
inverse of has developmental contribution from
Chris Mungall
RO:0002255
uberon
developmentally_contributes_to
developmentally_contributes_to
developmentally contributes to
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
Chris Mungall
David Osumi-Sutherland
Melissa Haendel
induced by
Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
GO:0001759
We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]
RO:0002256
uberon
developmentally_induced_by
developmentally_induced_by
sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
developmentally induced by
developmentally_induced_by
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.
GO:0001759
Inverse of developmentally induced by
Chris Mungall
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
false
Chris Mungall
In general you should not use this relation to make assertions - use one of the more specific relations below this one
RO:0002258
uberon
developmentally_preceded_by
developmentally_preceded_by
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
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.
acts upstream of
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.
affects
acts upstream of or within
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
Chris Mungall
replaces
RO:0002285
uberon
developmentally_replaces
developmentally_replaces
developmentally replaces
developmentally_replaces
Inverse of developmentally preceded by
Chris Mungall
developmentally succeeded by
'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue
Chris Mungall
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.
Chris Mungall
results_in_developmental_progression_of
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)
Chris Mungall
GOC:mtg_berkeley_2013
results_in_formation_of
results in formation of
cjm
holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
causally upstream of, positive effect
cjm
holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y
causally upstream of, negative effect
q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w.
Because part_of is transitive, inheres in is a sub-relation of inheres in part of
Chris Mungall
inheres in part of
true
A mereological relationship or a topological relationship
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
A relationship that holds between entities participating in some developmental process (GO:0032502)
Chris Mungall
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
Chris Mungall
catalyzes
executes
has
is catalyzing
is executing
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.
Chris Mungall
This is a grouping relation that collects relations used for the purpose of connecting structure and function
RO:0002328
uberon
functionally_related_to
functionally_related_to
functionally related to
functionally related to
this relation holds between c and p when c is part of some c', and c' is capable of p.
Chris Mungall
false
RO:0002329
uberon
part_of_structure_that_is_capable_of
part_of_structure_that_is_capable_of
part of structure that is capable of
part of structure that is capable of
true
c involved_in p if and only if c enables some process p', and p' is part of p
Chris Mungall
actively involved in
enables part of
RO:0002331
protein
involved_in
false
involved_in
involved in
involved_in
inverse of enables
Chris Mungall
enabled by
inverse of regulates
Chris Mungall
regulated by (processual)
regulated by
inverse of negatively regulates
Chris Mungall
negatively regulated by
inverse of positively regulates
Chris Mungall
positively regulated by
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
is member of
member part of
SIO
RO:0002350
uberon
member_of
member_of
member of
member of
has member is a mereological relation between a collection and an item.
SIO
RO:0002351
uberon
has_member
has_member
has member
has member
inverse of has input
Chris Mungall
RO:0002352
uberon
input_of
input_of
input of
input of
inverse of has output
Chris Mungall
RO:0002353
protein
uberon
output_of
false
output_of
output of
output of
output_of
Chris Mungall
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
Chris Mungall
attached to (anatomical structure to anatomical structure)
RO:0002371
uberon
attaches_to
attaches_to
attached to
attaches_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.
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.
Chris Mungall
Wikipedia:Insertion_(anatomy)
RO:0002373
uberon
has_muscle_insertion
has_muscle_insertion
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
has_muscle_insertion
We need to import uberon muscle into RO to use as a stricter domain constraint
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.
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.
Chris Mungall
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
https://github.com/obophenotype/uberon/issues/170
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.
Chris Mungall
drains into
drains to
tributary channel of
http://en.wikipedia.org/wiki/Tributary
http://www.medindia.net/glossary/venous_tributary.htm
This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)
RO:0002376
uberon
drains into
tributary_of
tributary_of
tributary of
tributary_of
http://en.wikipedia.org/wiki/Tributary
drains into
dbpowl:drainsTo
A lump of clay and a statue
x spatially_coextensive_with y if and inly if x and y have the same location
Chris Mungall
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
Chris Mungall
RO:0002380
uberon
branching_part_of
branching_part_of
branching part of
branching_part_of
FMA:85994
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).
Chris Mungall
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
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
Chris Mungall
RO:0002385
uberon
has_potential_to_developmentally_contribute_to
has_potential_to_developmentally_contribute_to
has potential to developmentally contribute to
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
Chris Mungall
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
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
Chris Mungall
RO:0002387
uberon
has_potential_to_develop_into
has_potential_to_develop_into
has potential to develop into
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
x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
Chris Mungall
RO:0002388
uberon
has_potential_to_directly_develop_into
has_potential_to_directly_develop_into
has potential to directly develop into
has potential to directly develop into
inverse of upstream of
Chris Mungall
causally downstream of
Chris Mungall
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.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
Chris Mungall
causally upstream of
p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
Chris Mungall
immediately causally upstream of
p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
Chris Mungall
influences (processual)
affects
causally upstream of or within
inverse of causally upstream of or within
Chris Mungall
causally downstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
Chris Mungall
involved in regulation of
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
Chris Mungall
involved in positive regulation of
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
Chris Mungall
involved in negative regulation of
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
Chris Mungall
involved in or reguates
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.
Chris Mungall
executes activity in
enables activity in
is active in
true
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.
GOC:cjm
GOC:dos
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.
Chris Mungall
RO:0002433
uberon
contributes_to_morphology_of
contributes_to_morphology_of
contributes to morphology of
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
Considering relabeling as 'pairwise interacts with'
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.
Chris Mungall
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.
in pairwise interaction with
interacts with
http://purl.obolibrary.org/obo/MI_0914
https://github.com/oborel/obo-relations/wiki/InteractionRelations
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.
Chris Mungall
binds
molecularly binds with
molecularly interacts with
http://purl.obolibrary.org/obo/MI_0915
Axiomatization to GO to be added later
Chris Mungall
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
phosphorylates
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.
Chris Mungall
molecularly controls
activity directly regulates activity of
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.
Chris Mungall
inhibits
molecularly decreases activity of
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.
Chris Mungall
activates
molecularly increases activity of
activity directly positively regulates activity of
Chris Mungall
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)
Chris Mungall
is symbiosis
'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
Chris Mungall
RO:0002473
uberon
composed_primarily_of
composed_primarily_of
composed primarily of
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.
Chris Mungall
has part that occurs in
true
Chris Mungall
is kinase activity
Chris Mungall
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 structure and 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).
Chris Mungall
RO:0002488
begins_to_exist_during
uberon
existence_starts_during
existence_starts_during
existence starts during
existence starts during
Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s.
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).
Chris Mungall
RO:0002489
uberon
existence_starts_with
existence_starts_with
existence starts with
Relation between continuant and occurrent, such that c comes into existence at the start of p.
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))
Chris Mungall
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.
existence overlaps
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).
Chris Mungall
RO:0002492
ceases_to_exist_during
uberon
existence_ends_during
existence_ends_during
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.
existence ends during
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.
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).
Chris Mungall
RO:0002493
uberon
existence_ends_with
existence_ends_with
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.
existence ends with
Relation between continuant and occurrent, such that c ceases to exist at the end of p.
x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships
Chris Mungall
RO:0002494
transforms from
uberon
transformation_of
transformation_of
transformation of
transforms from
SIO:000657
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
Chris Mungall
RO:0002495
direct_transformation_of
immediately transforms from
uberon
immediate_transformation_of
immediate_transformation_of
immediate transformation of
direct_transformation_of
immediately transforms from
SIO:000658
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).
Chris Mungall
RO:0002496
uberon
existence_starts_during_or_after
existence_starts_during_or_after
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.
existence starts during or after
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.
Chris Mungall
RO:0002497
uberon
existence_ends_during_or_before
existence_ends_during_or_before
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.
existence ends during or before
A relationship between a material entity and a process where the material entity has some causal role that influences the process
causal agent in 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.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between processes
Chris Mungall
depends on
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
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between 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.
Chris Mungall
has supporting framework
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).
RO:0002551
uberon
has sekeletal support
has supporting framework
has_skeleton
has_skeleton
has skeleton
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.
A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision.
Chris Mungall
causally influenced by (material entity to material entity)
causally influenced by
Chris Mungall
interaction relation helper property
https://github.com/oborel/obo-relations/wiki/InteractionRelations
Chris Mungall
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
Chris Mungall
causally influences (material entity to material entity)
causally influences
A relation that holds between elements of a musculoskeletal system or its analogs.
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes.
biomechanically related to
inverse of branching part of
Chris Mungall
RO:0002569
uberon
has_branching_part
has_branching_part
has branching part
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.
Chris Mungall
GOC:cjm
RO:0002571
uberon
lumen_of
lumen_of
lumen of
s is luminal space of x iff s is lumen_of x and s is an immaterial entity
Chris Mungall
RO:0002572
uberon
luminal_space_of
luminal_space_of
luminal space of
inverse of has skeleton
Chris Mungall
RO:0002576
uberon
skeleton_of
skeleton_of
skeleton of
Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
Chris Mungall
directly regulates (processual)
directly regulates
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
Chris Mungall
has part structure that is capable of
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.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
Chris Mungall
causal relation between material entity and a process
pyrethroid -> growth
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
capable of regulating
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
capable of negatively regulating
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.
capable of positively regulating
Inverse of 'causal agent in process'
process has causal agent
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.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
obsolete related via dependence to
true
Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.
directly positively regulates (process to process)
directly positively regulates
Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.
directly negatively regulates (process to process)
directly negatively regulates
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.
Melissa Haendel
RO:0003000
uberon
produces
produces
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
produces
a produced_by b iff some process that occurs_in b has_output a.
Melissa Haendel
RO:0003001
uberon
produced_by
produced_by
produced by
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.
cjm
2017-12-26T19:45:49Z
realized in response to stimulus
Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
cjm
2018-01-25T23:20:13Z
enables subfunction
cjm
2018-01-26T23:49:30Z
acts upstream of or within, positive effect
cjm
2018-01-26T23:49:51Z
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
cjm
2018-01-26T23:53:14Z
acts upstream of, positive effect
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
cjm
2018-01-26T23:53:22Z
acts upstream of, negative effect
cjm
2018-03-13T23:55:05Z
causally upstream of or within, negative effect
cjm
2018-03-13T23:55:19Z
causally upstream of or within, positive effect
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.
Austin Meier
Chris Mungall
David Osumi-Sutherland
Marie Angelique Laporte
triggered by process
realized in response to
https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit
triggered by process
RO:cjm
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*.
[072-ISO]
g-depends on
generically depends on
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*
[072-ISO]
is carrier of
vaccine immunization for host
vaccine immunization against microbe
Type of tissue or cell/the source of the material.
disease_ontology
derives_from
derives_from
Type of tissue or cell/the source of the material.
DO:lh
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.
uberon
anteriorly_connected_to
anteriorly connected to
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.
carries
uberon
channel_for
channel for
uberon
channels_from
channels_from
uberon
channels_into
channels_into
x is a conduit for y iff y passes through the lumen of x.
uberon
conduit_for
conduit for
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.
uberon
distally_connected_to
distally connected to
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.
uberon
existence_starts_and_ends_during
existence starts and ends during
uberon
extends_fibers_into
extends_fibers_into
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.
uberon
filtered_through
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
filtered through
a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s
add to RO
uberon
indirectly_supplies
indirectly_supplies
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.
uberon
posteriorly_connected_to
posteriorly connected to
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.
uberon
protects
protects
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.
uberon
proximally_connected_to
proximally connected to
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.
uberon
subdivision_of
placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B
subdivision of
.
uberon
transitively_anteriorly_connected_to
transitively anteriorly connected to
.
uberon
transitively_connected_to
transitively_connected to
.
uberon
transitively_distally_connected_to
transitively distally connected to
.
.
uberon
transitively_proximally_connected_to
transitively proximally connected to
.
has_disease_location
has_disease_location
entity
entity
实体
Entity
Entity
实体
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])
entity
entity
实体
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
per discussion with Barry Smith
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
continuant
continuant
常体
Continuant
Continuant
常体
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.
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) (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 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 (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]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
continuant
常体
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
occurrent
Occurrent
An entity that has temporal parts and that happens, unfolds or develops through time.
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
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.
per discussion with Barry Smith
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]
ic
IndependentContinuant
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
独立常体
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]
s-region
SpatialRegion
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
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.
per discussion with Barry Smith
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]
t-region
TemporalRegion
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
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
per discussion with Barry Smith
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]
2d-s-region
TwoDimensionalSpatialRegion
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
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]
st-region
SpatiotemporalRegion
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 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 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]
process
Process
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
bfo
BFO:0000015
process
process
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])
(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]
realizable
realizable
可实现的
RealizableEntity
RealizableEntity
可实现实体(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 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]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
realizable entity
可实现实体
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
0d-s-region
ZeroDimensionalSpatialRegion
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
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]
quality
Quality
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
bfo
BFO:0000019
quality
quality
性质
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]
sdc
sdc
SpecificallyDependentContinuant
SpecificallyDependentContinuant
特定依赖性常体(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 role of being a doctor
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
作为医生的角色
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.
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 (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]
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
specifically dependent continuant
特定依赖性常体
b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
per discussion with Barry Smith
(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]
role
Role
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
角色
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]
fiat-object
fiat-object-part
FiatObjectPart
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]
bfo
BFO:0000024
fiat object
fiat object part
fiat object part
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]
1d-s-region
OneDimensionalSpatialRegion
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 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]
object-aggregate
ObjectAggregate
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
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
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]
3d-s-region
ThreeDimensionalSpatialRegion
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
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]
site
Site
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
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]
object
Object
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])
bfo
BFO:0000030
object
object
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])
gdc
GenericallyDependentContinuant
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
普遍依赖性常体
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]
function
Function
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
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]
p-boundary
ProcessBoundary
the boundary between the 2nd and 3rd year of your life.
p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
process boundary
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]
1d-t-region
OneDimensionalTemporalRegion
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 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]
material
MaterialEntity
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
bfo
BFO:0000040
material entity
material entity
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]
cf-boundary
ContinuantFiatBoundary
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
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])
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.
(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]
immaterial
ImmaterialEntity
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
1d-cf-boundary
OneDimensionalContinuantFiatBoundary
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
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]
process-profile
ProcessProfile
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
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]
2
r-quality
RelationalQuality
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.
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
2
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]
2d-cf-boundary
TwoDimensionalContinuantFiatBoundary
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
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]
0d-cf-boundary
ZeroDimensionalContinuantFiatBoundary
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
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.
requested by Melanie Courtot
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]
0d-t-region
ZeroDimensionalTemporalRegion
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 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]
history
History
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
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])
anatomical entity
connected anatomical structure
material anatomical entity
immaterial anatomical entity
multi-cell-part structure
neuron projection bundle
multicellular anatomical structure
biological entity
molecular entity
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well
molecular entity
chebi_ontology
entidad molecular
entidades moleculares
entite moleculaire
molecular entities
molekulare Entitaet
CHEBI:23367
molecular entity
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
fake:2
molecular entity
IUPAC
entidad molecular
IUPAC
entidades moleculares
IUPAC
entite moleculaire
IUPAC
molecular entities
IUPAC
molekulare Entitaet
ChEBI
A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
chemical entity
chebi_ontology
CHEBI:24431
chemical entity
chemical entity
UniProt
a maintaining cell culture process that keeps cell line cell alive and actively cultured.
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。
YH
YH
cell line cell culturing
cell line cell culturing
细胞系细胞培养
cell line cell
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
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
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
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.
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。
cell line cell
cell line cell
细胞系细胞
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)
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
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.
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
adherent cell line culturing
贴壁细胞系培养
a role that inheres in a cell line repository organization.
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
SS, YH
cell line repository role
cell line repository role
细胞库角色
an organization that serves as a repository of cell lines.
an organization that serves as a repository of cell lines.
一个作为细胞系存储库的组织。
SS, YH
SS, YH
cell line repository
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
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
adherent-patchy cell line culturing
贴壁斑片状细胞培养
loosely adherent cell line culturing
loosely adherent cell line culturing
松散贴壁细胞培养
immortal cell line cell
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.
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
Yongqun He, Matthew Brush, Allen Xiang, Asiyah Yu Lin, Sirarat Sarntivijai, James Malone, Jie Zheng, Tomasz Adamusiak
continuous cell line cell
continuous cell line cell
permanent cell line cell
permanent cell line cell
永久细胞系细胞
连续细胞系细胞
immortal cell line cell
immortal cell line cell
永生细胞系细胞
a cell culture growth mode that indicates a cell needs to adhere to a cell culture plate to grow.
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
YH
YH
adherent cell culture growth mode
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.
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
YH
YH
suspension cell culture growth mode
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.
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。
YH
YH
cell culture growth mode
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).
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).
cell line
细胞系
mixed adherent and suspension cell line culturing
mixed adherent and suspension cell line culturing
混合贴壁悬浮细胞培养
mixed suspension
clusters in suspension cell line culturing
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.
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
Yue Liu, Yongqun He
immortal mouse cell line
永生的小鼠细胞系
immortal mouse cell line cell
immortal mouse cell line cell
永生的小鼠细胞系细胞
YH
a immortal cell line that is dervied from mouse macrophage.
immortal mouse macrophage cell line
a cell line that is derived from motile cell
a cell line that is derived from motile cell
源自运动细胞的细胞系
ZX, YH
ZX, YH
immortal motile cell line
immortal motile cell line
永生的游动细胞系
immortal motile cell line cell
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
a immortal motile cell line that is derived from leukocyte
源自白细胞的永生游动细胞系
ZX, YH
ZX, YH
immortal leukocyte cell line
immortal leukocyte cell line
永生的白细胞系
immortal leukocyte cell line cell
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
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
ZX, YH
ZX, YH
immortal myeloid leukocyte cell line
immortal myeloid leukocyte cell line
永生的髓样白血球细胞系
immortal myeloid leukocyte cell line cell
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
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
ZX, YH
ZX, YH
immortal monocyte cell line
immortal monocyte cell line
永生的单核细胞系
immortal monocyte cell line cell
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
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
ZX, YH
ZX, YH
immortal nongranular leukocyte cell line
immortal nongranular leukocyte cell line
永生的无颗粒白细胞细胞系
immortal nongranular leukocyte cell line cell
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
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
ZX, YH
ZX, YH
immortal eukaryotic cell line cell
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
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
ZX, YH
ZX, YH
immortal animal cell line
immortal animal cell line
永生的动物细胞系
immortal animal cell line cell
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
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
ZX, YH
ZX, YH
immortal epithelial cell line cell
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
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
ZX, YH
ZX, YH
immortal hematopoietic cell line
immortal hematopoietic cell line
永生的造血细胞系
immortal hematopoietic cell line cell
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
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
ZX, YH
ZX, YH
immortal myeloid cell line
immortal myeloid cell line
永生的骨髓细胞系
immortal myeloid cell line cell
immortal myeloid cell line cell
永生的骨髓细胞系细胞
a cell line that is derived from somatic cell
a cell line that is derived from somatic cell
源自体细胞的细胞系
ZX, YH
ZX, YH
immortal somatic cell line cell
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.
An immortal cell line cell that derives from pair of lungs.
源自一对肺的永生细胞系细胞。
Yue Liu, Yongqun He
Yue Liu, Yongqun He
immortal lung-derived cell line cell
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.
An immortal cell line cell that derives from kidney.
源自肾的永生细胞系细胞。
Yue Liu, Yongqun He
Yue Liu, Yongqun He
immortal kidney-derived cell line cell
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.
An immortal cell line cell that derives from colon.
源自结肠的永生细胞系细胞。
Yue Liu, Yongqun He
Yue Liu, Yongqun He
immortal colon-derived cell line cell
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.
An immortal cell line cell that derives from female gonad.
源自雌性性腺的永生细胞系细胞。
Yue Liu, Yongqun He
Yue Liu, Yongqun He
immortal female gonad-derived cell line cell
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.
An immortal cell line cell that derives from stomach.
源自胃的永生细胞系细胞。
Yue Liu, Yongqun He
Yue Liu, Yongqun He
immortal stomach-derived cell line cell
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.
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。
Yue Liu, Yongqun He
Yue Liu, Yongqun He
immortal uterine cervix-derived epithelial cell line cell
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.
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。
Yue Liu, Yongqun He
Yue Liu, Yongqun He
immortal human lung-derived cell line cell
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.
An immortal cell line cell that derives from human.
源自人的永生细胞系细胞。
Yue Liu, Yongqun He
Yue Liu, Yongqun He
immortal human cell line cell
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.
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。
Yue Liu, Yongqun He
Yue Liu, Yongqun He
immortal human colon-derived cell line cell
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.
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。
Yue Liu, Yongqun He
Yue Liu, Yongqun He
immortal vervet monkey kidney-derived cell line cell
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.
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。
Yue Liu, Yongqun He
Yue Liu, Yongqun He
immortal human stomach-derived cell line cell
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.
An immortal epithelial cell line cell that derives from human.
源自人的永生上皮细胞系细胞。
Yue Liu, Yongqun He
Yue Liu, Yongqun He
immortal human epithelial cell line cell
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.
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。
Yue Liu, Yongqun He
Yue Liu, Yongqun He
immortal human uterine cervix-derived epithelial cell line cell
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.
An immortal monocyte cell line cell that derives from human.
源自人的永生单核细胞系细胞。
Yue Liu, Yongqun He
Yue Liu, Yongqun He
immortal human monocyte cell line cell
immortal human monocyte cell line cell
永生的人单核细胞系细胞
LCL-1601
LCL-1601
A549
A549
A549 cell
A549 cell
A549 细胞
ATCC: CCL-185
ATCC: CCL-185
CHEMBL: CHEMBL3307651
CHEMBL: CHEMBL3307651
CVCL: CVCL_0023
CVCL: CVCL_0023
EFO: EFO_0001086
EFO: EFO_0001086
HyperCLDB: cl207
HyperCLDB: cl207
LCL-1893
LCL-1893
AGS
AGS
AGS cell
AGS cell
AGS 细胞
ATCC: CRL-1739
ATCC: CRL-1739
CHEMBL: CHEMBL3308078
CHEMBL: CHEMBL3308078
CVCL: CVCL_0139
CVCL: CVCL_0139
EFO: EFO_0002109
EFO: EFO_0002109
LCL-1170
LCL-1170
Caco-2
Caco-2
disease: colorectal adenocarcinoma
disease: colorectal adenocarcinoma
疾病:结肠直肠腺癌
Caco-2 cell
Caco-2 cell
Caco-2 细胞
ATCC: HTB-37
ATCC: HTB-37
CHEMBL: CHEMBL3307519
CHEMBL: CHEMBL3307519
CVCL: CVCL_0025
CVCL: CVCL_0025
EFO: EFO_0001099
EFO: EFO_0001099
HyperCLDB: cl618
HyperCLDB: cl618
MeSH: D018938
MeSH: D018938
CHO
CHO
Chinese Hamster Ovary cell
Chinese Hamster Ovary cell
中国仓鼠卵巢细胞
CHO cell
CHO cell
CHO 细胞
HyperCLDB: cl721
HyperCLDB: cl721
MeSH: D016466
MeSH: D016466
LCL-1226
Detroit 562
https://www.atcc.org/products/all/CCL-138.aspx
disease: carcinoma (pharynx primary)
Detroit 562 cell
ATCC: CCL-138
CHEMBL: CHEMBL3308486
CVCL: CVCL_1171
ECACC: 87042205
EFO: EFO_0002170
LCL-1512
LCL-1512
HeLa
HeLa
WEB: http://en.wikipedia.org/wiki/HeLa
WEB: http://en.wikipedia.org/wiki/HeLa
WEB: http://www.atcc.org/products/all/CCL-2.aspx
WEB: http://www.atcc.org/products/all/CCL-2.aspx
WEB: https://www.ncbi.nlm.nih.gov/pubmed/12001993
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.
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 cell
HeLa 细胞
ATCC: CCL-2
ATCC: CCL-2
CHEMBL: CHEMBL3308376
CHEMBL: CHEMBL3308376
EFO: EFO_0001185
EFO: EFO_0001185
HyperCLDB: cl1601
HyperCLDB: cl1601
MeSH: D006367
MeSH: D006367
RRID:CVCL_0030
RRID:CVCL_0030
HEp-2
HEp-2 cell
ATCC: CCL-23
INT 407
INT 407 cell
HyperCLDB: cl2897
J774A.1
J774A.1
J 774A.1
J774A.1 cell
J774A.1 cell
J774A.1 细胞
ATCC: TIB-67
ATCC: TIB-67
HyperCLDB: cl2928
HyperCLDB: cl2928
LS 174T
LS 174T
disease: colorectal adenocarcinoma
disease: colorectal adenocarcinoma
疾病:大肠腺癌
LS 174T cell
LS 174T cell
LS 174T 细胞
ATCC: CL-188
ATCC: CL-188
NCI-H292
NCI-H292
disease: mucoepidermoid pulmonary carcinoma
disease: mucoepidermoid pulmonary carcinoma
疾病:黏液表皮样肺癌
NCI-H292 cell
NCI-H292 cell
NCI-H292 细胞
ATCC: CRL-1848
ATCC: CRL-1848
LCL-1072
LCL-1072
THP-1
THP-1
THP1
THP1
THP-1 cell
THP-1 cell
THP-1 细胞
ATCC: TIB-202
ATCC: TIB-202
CHEMBL: CHEMBL3307574
CHEMBL: CHEMBL3307574
CVCL: CVCL_0006
CVCL: CVCL_0006
EFO: EFO_0001253
EFO: EFO_0001253
HyperCLDB: cl4514
HyperCLDB: cl4514
Vero
Vero
Vero cell
Vero cell
Vero 细胞
ATCC: CCL-81
ATCC: CCL-81
HyperCLDB: cl4644
HyperCLDB: cl4644
MeSH: D014709
MeSH: D014709
LCL-1601
A immortal human cell line cell that has the characteristics: Lung carcinoma, refer to ATCC CCL185
RIKEN Cell bank Team Yongqun He
A549
RCB0098
Derived from tissue: lung in animal: human.
Originator: Giard, D. J.
Register: Abe, Shin-ichiro
RCB0098 cell
ATCC: CCL-185
cell
cell
PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
CALOHA:TS-2035
FMA:68646
GO:0005623
KUPO:0000002
VHOG:0001533
WBbt:0004017
XAO:0003012
cell
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
cell
cell type
cell type
细胞
细胞类型
primary cultured cell
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
primary cultured cell
原代培养细胞
native cell
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).
CARO:0000013
cell in vivo
cell
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).
native cell
cultured cell
A cell in vitro that is or has been maintained or propagated as part of a cell culture.
cell
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.
cultured cell
epithelial cell
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.
BTO:0000414
CALOHA:TS-2026
CARO:0000077
FBbt:00000124
FMA:66768
WBbt:0003672
epitheliocyte
cell
epithelial cell
epithelial cell
上皮细胞
A cell found predominately in the blood.
FMA:62844
cell
blood cell
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.
BTO:0001176
CALOHA:TS-0278
FMA:66772
endotheliocyte
cell
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].
endothelial cell
A cell that moves by its own activities.
cell
motile cell
motile cell
游动细胞
macrophage
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.
BTO:0000801
CALOHA:TS-0587
FMA:63261
FMA:83585
histiocyte
cell
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
macrophage
巨噬细胞
B cell
A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity.
B cell
cell
eukaryotic cell
eukaryotic cell
真核细胞
lymphocyte
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.
BTO:0000775
CALOHA:TS-0583
FMA:62863
VHOG:0001535
cell
Editors note: consider adding taxon constraint to vertebrata (PMID:18025161)
lymphocyte
cell
animal cell
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.
BTO:0000876
CALOHA:TS-0638
FMA:62864
cell
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
monocyte
单核细胞
experimentally modified cell in vitro
A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
experimentally modified cell in vitro
An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
BTO:0000751
CALOHA:TS-0549
FMA:62852
immune cell
leucocyte
white blood cell
cell
leukocyte
leukocyte
白血球
A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.
BTO:0001441
CALOHA:TS-0647
cell
myeloid cell
myeloid cell
骨髓细胞
A cell of the monocyte, granulocyte, or mast cell lineage.
cell
myeloid leukocyte
myeloid leukocyte
骨髓白细胞
mononuclear cell
A leukocyte with a single non-segmented nucleus in the mature form.
mononuclear cell
A cell of a hematopoietic lineage.
BTO:0000574
CALOHA:TS-2017
FMA:70366
FMA:83598
haematopoietic cell
haemopoietic cell
hemopoietic cell
cell
hematopoietic cell
hematopoietic cell
造血干细胞
A leukocyte that lacks granules.
tmeehan
2010-07-22T11:30:33Z
FMA:62855
agranular leukocyte
cell
nongranular leukocyte
nongranular leukocyte
无颗粒白细胞
An epithelial cell of the bronchus.
tmeehan
2010-09-20T02:00:00Z
BTO:0002922
cell
bronchial epithelial cell
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.
tmeehan
2010-09-22T09:27:05Z
primitive erythroblast
primitive erythrocyte
primitive erythroid cell
cell
primitive red blood cell
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).
tmeehan
2010-09-24T09:44:42Z
BTO:0001268
FMA:72300
WBbt:0008378
cell
somatic cell
somatic cell
体细胞
An epithelial cell of the intestine.
tmeehan
2011-03-01T05:18:31Z
cell
intestinal epithelial cell
Cell of the nasopharyngeal epithelium.
CALOHA:TS-2398
nasopharynx respiratory epithelial cells
nasopharyngeal epithelial cell
Any blood vessel endothelial cell that is part of a microvascular endothelium.
TermGenie
2014-06-04T15:07:42Z
cell
CL:2000008
microvascular endothelial cell
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).
disease_ontology
DOID:0050155
sensory system disease
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).
url:http://en.wikipedia.org/wiki/Sensory_system
A respiratory system disease which involves the lower respiratory tract.
ICD9CM:478.1
ICD9CM:478.19
UMLS_CUI:C0029581
disease_ontology
DOID:0050161
lower respiratory tract disease
A respiratory system disease which involves the lower respiratory tract.
url:http://en.wikipedia.org/wiki/lower_respiratory_tract
An organ system cancer located_in the respiratory system that is characterized by uncontrolled cellular proliferation in the respiratory tract.
disease_ontology
DOID:0050615
respiratory system cancer
An organ system cancer located_in the respiratory system that is characterized by uncontrolled cellular proliferation in the respiratory tract.
url:http://en.wikipedia.org/wiki/Respiratory_tract_neoplasm
A cancer that is classified based on the organ it starts in.
snadendla
2011-06-13T03:28:33Z
MESH:D009371
disease_ontology
DOID:0050686
organ system cancer
A cancer that is classified based on the organ it starts in.
url:http://cancerguide.org/basic.html
A cancer that is classified by the type of cell from which it is derived.
snadendla
2011-06-13T03:28:50Z
disease_ontology
DOID:0050687
cell type cancer
A cancer that is classified by the type of cell from which it is derived.
url:http://cancerguide.org/basic.html
url:http://en.wikipedia.org/wiki/Cancer
A large intestine cancer that is located_in the terminal part of the large intestine.
snadendla
2011-06-14T01:34:36Z
disease_ontology
DOID:0050688
anal canal cancer
A large intestine cancer that is located_in the terminal part of the large intestine.
url:http://en.wikipedia.org/wiki/Anal_canal
An eye and adnexa disease that is located_in the adnexa of the eye.
lschriml
2013-12-05T12:55:42Z
disease_ontology
DOID:0050815
eye adnexa disease
An eye and adnexa disease that is located_in the adnexa of the eye.
url:http://en.wikipedia.org/wiki/Accessory_visual_structures
A heart disease that is located_in the innermost layer of tissue that lines the chambers of the heart.
lschriml
2014-02-12T01:53:42Z
disease_ontology
DOID:0050825
endocardium disease
A heart disease that is located_in the innermost layer of tissue that lines the chambers of the heart.
url:http://en.wikipedia.org/wiki/Endocardium
url:http://people.upei.ca/lmiller/2009_CV_Endocardial_Pathology/ENDOCARDIUM-2009.pdf
A vascular disease that is located_in an artery.
lschriml
2014-02-12T03:08:35Z
disease_ontology
DOID:0050828
artery disease
A vascular disease that is located_in an artery.
url:http://en.wikipedia.org/wiki/Artery#Pathology
An organ system cancer located_in the muscular and skeletal organs and characterized by uncontrolled cellular proliferation of the musculoskeletal organs.
lschriml
2011-07-15T02:30:51Z
DOID:0060124
skeletal system cancer
disease_ontology
DOID:0060100
musculoskeletal system cancer
An organ system cancer located_in the muscular and skeletal organs and characterized by uncontrolled cellular proliferation of the musculoskeletal organs.
url:http://en.wikipedia.org/wiki/Musculoskeletal_system#Diseases_and_disorders
A connective tissue tumor that can be a benign chondroma or a maligannt chondrosarcoma.
lschriml
2011-07-20T01:40:49Z
disease_ontology
DOID:0060102
cartilage cancer
A connective tissue tumor that can be a benign chondroma or a maligannt chondrosarcoma.
url:https://en.wikipedia.org/wiki/Cartilage_tumor
A nervous system cancer that is located in the sensory system.
lschriml
2011-07-25T01:51:56Z
disease_ontology
DOID:0060116
sensory system cancer
A nervous system cancer that is located in the sensory system.
url:http://en.wikipedia.org/wiki/Sensory_system
A disease of anatomical entity that is located_in the thoracic cavity.
lschriml
2011-07-25T02:23:47Z
disease_ontology
DOID:0060118
thoracic disease
A disease of anatomical entity that is located_in the thoracic cavity.
url:http://en.wikipedia.org/wiki/Thoracic_cavity
A gastrointestinal system cancer that is located_in the pharynx.
lschriml
2011-07-27T01:26:34Z
MESH:D010610
NCI:C3325
SNOMEDCT_US_2018_03_01:95001001
UMLS_CUI:C0031347
pharyngeal neoplasm
pharynx neoplasm
disease_ontology
pharyngeal cancer
DOID:0060119
pharynx cancer
A gastrointestinal system cancer that is located_in the pharynx.
url:http://en.wikipedia.org/wiki/Pharynx
An organ system cancer that is located_in the skin, hair and nails.
lschriml
2011-07-27T02:31:34Z
disease_ontology
DOID:0060122
integumentary system cancer
An organ system cancer that is located_in the skin, hair and nails.
url:http://en.wikipedia.org/wiki/Integumentary_system
A musculoskeletal system disease that affects the muscles.
disease_ontology
DOID:0080000
muscular disease
A musculoskeletal system disease that affects the muscles.
url:http://www.nlm.nih.gov/medlineplus/muscledisorders.html
A connective tissue disease that affects the structure or development of bone or causes an impairment of normal bone function.
DOID:1290
ICD10CM:M89.9
MESH:D001847
SNOMEDCT_US_2018_03_01:76069003
UMLS_CUI:C0005940
disease_ontology
skeletal disease
DOID:0080001
bone disease
A connective tissue disease that affects the structure or development of bone or causes an impairment of normal bone function.
url:http://en.wikipedia.org/wiki/Bone_disease
An eye disease that affects the cornea, which is the transparent surface of the eye that assists in light refraction.
DOID:2284
ICD10CM:H18.9
ICD9CM:371.9
MESH:D003316
NCI:C26731
SNOMEDCT_US_2018_03_01:15250008
UMLS_CUI:C0010034
disease_ontology
DOID:10124
corneal disease
An eye disease that affects the cornea, which is the transparent surface of the eye that assists in light refraction.
url:https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C26731
A gastrointestinal system cancer that is located_in the intestine.
ICD10CM:C26.0
ICD9CM:159.0
MESH:D007414
NCI2004_11_17:C4572
NCI:C4572
SNOMEDCT_US_2018_03_01:93838000
UMLS_CUI:C0346627
malignant intestinal tumors
malignant neoplasm of intestine
disease_ontology
DOID:10155
intestinal cancer
A gastrointestinal system cancer that is located_in the intestine.
url:http://en.wikipedia.org/wiki/Intestine
A gastrointestinal system cancer that is located_in the stomach.
DOID:10539
DOID:10542
DOID:10543
DOID:4713
GARD:7704
ICD10CM:C16
ICD10CM:C16.2
ICD10CM:C16.5
ICD10CM:C16.6
ICD10CM:C16.9
ICD9CM:151
ICD9CM:151.4
ICD9CM:151.5
ICD9CM:151.6
ICD9CM:151.9
MESH:D013274
NCI:C3387
NCI:C9331
OMIM:137215
OMIM:613659
SNOMEDCT_US_2018_03_01:93717002
SNOMEDCT_US_2018_03_01:93818001
SNOMEDCT_US_2018_03_01:93867004
SNOMEDCT_US_2018_03_01:94074003
UMLS_CUI:C0024623
UMLS_CUI:C0038356
UMLS_CUI:C0153421
UMLS_CUI:C0153422
UMLS_CUI:C0153423
Ca body - stomach
Ca lesser curvature - stomach
ca greater curvature of stomach
gastric cancer
gastric neoplasm
malignant neoplasm of body of stomach
malignant neoplasm of lesser curve of stomach
malignant tumor of body of stomach
malignant tumor of greater curve of stomach
malignant tumor of lesser curve of stomach
disease_ontology
DOID:10534
OMIM mapping confirmed by DO. [SN].
stomach cancer
A gastrointestinal system cancer that is located_in the stomach.
url:http://cancergenome.nih.gov/cancersselected/stomach-esophagealcancer
url:http://en.wikipedia.org/wiki/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.
ICD10CM:H25-H28
ICD10CM:H27.9
MESH:D007905
NCI:C26812
SNOMEDCT_US_2018_03_01:10810001
UMLS_CUI:C0023308
disease_ontology
DOID:110
lens disease
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.
url:https://en.wikipedia.org/wiki/Lens_(anatomy)
A female reproductive system disease that is located_in the ovary.
MESH:D010049
NCI:C26841
SNOMEDCT_US_2018_03_01:5552004
UMLS_CUI:C0029928
disease_ontology
DOID:1100
ovarian disease
A female reproductive system disease that is located_in the ovary.
url:https://medlineplus.gov/ovariandisorders.html
An urinary system cancer that results_in malignant growth located_in the urinary bladder.
DOID:5428
GARD:12210
ICD10CM:C67
ICD10CM:C67.9
ICD9CM:188
ICD9CM:188.9
KEGG:05219
MESH:D001749
NCI2004_11_17:C2901
NCI:C2901
NCI:C9334
OMIM:109800
SNOMEDCT_US_2018_03_01:93689003
UMLS_CUI:C0005684
UMLS_CUI:C0005695
bladder cancer
tumor of the bladder
disease_ontology
DOID:11054
OMIM mapping confirmed by DO. [SN].
urinary bladder cancer
An urinary system cancer that results_in malignant growth located_in the urinary bladder.
url:http://en.wikipedia.org/wiki/Bladder_cancer
A cardiovascular system disease that involves the heart.
ICD10CM:I51.9
ICD9CM:429.9
MESH:D006331
NCI:C3079
SNOMEDCT_US_2018_03_01:56265001
UMLS_CUI:C0018799
disease_ontology
DOID:114
heart disease
A cardiovascular system disease that involves the heart.
url:http://en.wikipedia.org/wiki/Heart_disease
A female reproductive system disease characterized by the growth of endometrial tissue that is located_in the fallopian tube.
ICD10CM:N80.2
ICD9CM:617.2
ICD9CM_2006:617.2
NCI:C26763
SNOMEDCT_US_2018_03_01:22611009
UMLS_CUI:C0014177
Endometriosis of fallopian tube
disease_ontology
DOID:11424
fallopian tube endometriosis
A female reproductive system disease characterized by the growth of endometrial tissue that is located_in the fallopian tube.
url:https://en.wikipedia.org/wiki/Endometriosis
A female reproductive system disease characterized by the growth of endometrial tissue that is located_in the intestine.
ICD10CM:N80.5
ICD9CM:617.5
SNOMEDCT_US_2018_03_01:5562006
UMLS_CUI:C0156347
disease_ontology
DOID:11428
endometriosis of intestine
A female reproductive system disease characterized by the growth of endometrial tissue that is located_in the intestine.
url:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2653346/
A female reproductive system disease characterized by the growth of endometrial tissue that is located_in the ovary.
DOID:11426
ICD10CM:N80.1
ICD9CM:617.1
NCI:C27628
SNOMEDCT_US_2018_03_01:31007005
UMLS_CUI:C0156344
ovarian endometriosis
disease_ontology
DOID:11432
endometriosis of ovary
A female reproductive system disease characterized by the growth of endometrial tissue that is located_in the ovary.
url:https://en.wikipedia.org/wiki/Endometriosis
A cardiovascular cancer located_in the heart.
DOID:9918
GARD:2619
ICD10CM:C38.0
ICD9CM:164.1
MESH:D006338
NCI2004_11_17:C3081
NCI2004_11_17:C3548
NCI:C3081
NCI:C3548
SNOMEDCT_US_2018_03_01:93825008
UMLS_CUI:C0018809
UMLS_CUI:C0153500
Cardiac tumor
Tumour of heart
malignant Cardiac tumor
malignant neoplasm of heart
disease_ontology
DOID:117
heart cancer
A cardiovascular cancer located_in the heart.
url:http://en.wikipedia.org/wiki/Heart_cancer
ICD10CM:C67.5
ICD9CM:188.5
SNOMEDCT_US_2018_03_01:94124002
UMLS_CUI:C0153613
malignant neoplasm of urinary bladder neck
malignant tumor of bladder neck
disease_ontology
DOID:11809
bladder neck cancer
A urinary system cancer that is located_in the ureter.
ICD10CM:C66
ICD9CM:189.2
MESH:D014516
NCI2004_11_17:C7543
NCI:C7543
OMIM:191600
SNOMEDCT_US_2018_03_01:94121005
UMLS_CUI:C0153619
malignant tumour of ureter
malignant ureteral tumor
disease_ontology
DOID:11819
OMIM mapping confirmed by DO. [SN].
ureter cancer
A urinary system cancer that is located_in the ureter.
url:http://en.wikipedia.org/wiki/Ureter_cancer
A female reproductive system cancer that is located_in the vagina.
DOID:1902
CSP2005:2016-2004
GARD:9348
ICD10CM:C52
ICD9CM:184.0
ICD9CM_2006:184.0
MESH:D014625
NCI2004_11_17:C3437
NCI2004_11_17:C7410
NCI:C3437
NCI:C7410
UMLS_CUI:C0042237
UMLS_CUI:C0042258
malignant neoplasm of vagina
malignant tumor of vagina
malignant vaginal tumor
neoplasm of vagina
vagina neoplasm
vaginal tumor
disease_ontology
DOID:119
vaginal cancer
A female reproductive system cancer that is located_in the vagina.
url:http://www.cancer.gov/dictionary?CdrID=523460
A respiratory system cancer that is located_in the trachea.
ICD10CM:C33
ICD9CM:162.0
MTH:NOCODE
NCI2004_11_17:C9346
NCI:C9346
UMLS_CUI:C0153489
disease_ontology
DOID:11920
tracheal cancer
A respiratory system cancer that is located_in the trachea.
url:http://en.wikipedia.org/wiki/Lung_cancer
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.
CSP2005:2005-4325
GARD:12425
MESH:D006258
MTH:NOCODE
NCI:C3077
UMLS_CUI:C0018671
head and neck neoplasm
head and neck tumours
head/neck neoplasm
tumor of head and neck
disease_ontology
DOID:11934
head and neck cancer
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.
url:http://apps.who.int/bookorders/anglais/detart1.jsp?sesslan=1&codlan=1&codcol=70&codcch=9
url:http://en.wikipedia.org/wiki/Head_and_neck_cancer
url:http://www.cancer.gov/cancertopics/factsheet/Sites-Types/head-and-neck
url:http://www.cancer.gov/dictionary?CdrID=257519
url:http://www.iarc.fr/en/publications/pdfs-online/pat-gen/bb9/index.php
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.
DOID:1244
DOID:1281
ICD10CM:C57
ICD9CM:184
MESH:D005833
NCI2004_11_17:C4913
NCI:C3053
NCI:C4913
UMLS_CUI:C0017416
UMLS_CUI:C0153585
UMLS_CUI:C0699889
female reproductive cancer
malignant Gynecologic tumor
malignant neoplasm of female genital organ
disease_ontology
DOID:120
female reproductive organ cancer
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.
url:http://en.wikipedia.org/wiki/Template:Female_genital_neoplasia
url:http://www.wrongdiagnosis.com/g/genital_system_cancer/intro.htm
A female reproductive system disease that is located_in the vagina.
MESH:D014623
NCI:C26910
SNOMEDCT_US_2018_03_01:25658005
UMLS_CUI:C0042251
disease_ontology
DOID:121
vaginal disease
A female reproductive system disease that is located_in the vagina.
url:https://en.wikipedia.org/wiki/Vaginal_disease
ICD10CM:C18.7
ICD9CM:153.3
MESH:D012811
SNOMEDCT_US_2018_03_01:94006002
UMLS_CUI:C0153436
Ca sigmoid colon
malignant tumor of sigmoid colon
disease_ontology
DOID:12192
sigmoid colon cancer
A cancer that affects the blood or bone marrow characterized by an abnormal proliferation of blood cells.
DOID:9145
ICD10CM:C95
ICD10CM:C95.9
ICD10CM:C95.90
ICD9CM:208
ICD9CM:208.9
MESH:D007938
NCI:C3161
SNOMEDCT_US_2018_03_01:87163000
SNOMEDCT_US_2018_03_01:93143009
UMLS_CUI:C0023418
disease_ontology
DOID:1240
leukemia
A cancer that affects the blood or bone marrow characterized by an abnormal proliferation of blood cells.
url:http://en.wikipedia.org/wiki/Leukemia
url:http://www.cancer.gov/dictionary?CdrID=45343
An eye disease that involves the globe of the eye.
ICD10CM:H44.39
ICD9CM:360.29
UMLS_CUI:C0154780
disease_ontology
DOID:1242
globe disease
An eye disease that involves the globe of the eye.
url:https://en.wikipedia.org/wiki/Globe_(human_eye)
A vascular disease that is located_in the capillaries.
ICD10CM:I78
ICD10CM:I78.9
ICD9CM:448
SNOMEDCT_US_2018_03_01:57223003
SNOMEDCT_US_2018_03_01:58729003
UMLS_CUI:C0155765
disease of capillaries
disease_ontology
DOID:1271
capillary disease
A vascular disease that is located_in the capillaries.
url:http://en.wikipedia.org/wiki/Capillary#Pathophysiology
DOID:12760
ICD10CM:C69.3
ICD9CM:190.6
MESH:D002830
NCI2004_11_17:C2949
NCI2004_11_17:C3566
NCI:C2949
NCI:C3566
SNOMEDCT_US_2018_03_01:93755007
UMLS_CUI:C0008523
UMLS_CUI:C0153630
Choroidal tumor
choroid neoplasm
malignant tumor of choroid
malignant tumor of the Choroid
neoplasm of choroid
disease_ontology
DOID:12759
choroid cancer
MESH:D012002
SNOMEDCT_US_2018_03_01:5964004
UMLS_CUI:C0034882
disease_ontology
DOID:1285
rectal disease
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.
DOID:73
ICD9CM:429.2
MESH:D002318
NCI:C2931
SNOMEDCT_US_2018_03_01:49601007
UMLS_CUI:C0007222
disease of subdivision of hemolymphoid system
disease_ontology
DOID:1287
cardiovascular system disease
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.
url:http://en.wikipedia.org/wiki/Circulatory_system
A hematologic cancer located_in the central nervous system.
NCI2004_11_17:C5440
NCI:C5440
UMLS_CUI:C1332884
Leukemia of the CNS
disease_ontology
DOID:12969
central nervous system leukemia
A hematologic cancer located_in the central nervous system.
url:http://www.springerlink.com/content/gl61tx644217n938/
A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain.
DOID:2125
DOID:2126
DOID:3543
DOID:6649
DOID:911
CSP2005:2006-2736
ICD10CM:C71
ICD10CM:C71.9
ICD9CM:191
ICD9CM:191.9
ICD9CM:239.6
MESH:D001932
NCI2004_11_17:C2907
NCI2004_11_17:C3568
NCI2004_11_17:C4952
NCI2004_11_17:C4954
NCI2004_11_17:C5115
NCI2004_11_17:C7710
NCI:C2907
NCI:C3568
NCI:C4952
NCI:C4954
NCI:C5115
NCI:C7710
SNOMEDCT_US_2018_03_01:93727008
UMLS_CUI:C0006118
UMLS_CUI:C0153633
UMLS_CUI:C0220624
UMLS_CUI:C0750974
UMLS_CUI:C0750979
UMLS_CUI:C1334557
BT - Brain tumour
adult brain tumor
adult malignant brain neoplasm
brain neoplasm
brain neoplasm, adult
malignant brain tumour
malignant primary brain neoplasm
malignant primary brain tumor
malignant tumor of Brain
malignant tumor of adult brain
neoplasm of brain
primary brain neoplasm
primary brain tumor
primary malignant neoplasm of brain
tumor of the Brain
disease_ontology
DOID:1319
brain cancer
A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain.
url:http://www.cancer.gov/dictionary?CdrID=387264
A respiratory system cancer that is located_in the lung.
DOID:13075
DOID:1322
DOID:9881
ICD10CM:C34.1
ICD10CM:C34.2
ICD10CM:C34.3
ICD9CM:162.3
ICD9CM:162.4
ICD9CM:162.5
ICD9CM:162.8
OMIM:211980
OMIM:608935
OMIM:612571
OMIM:612593
OMIM:614210
UMLS_CUI:C0024624
UMLS_CUI:C0153491
UMLS_CUI:C0153492
UMLS_CUI:C0153493
disease_ontology
lung neoplasm
DOID:1324
lung cancer
A respiratory system cancer that is located_in the lung.
url:http://en.wikipedia.org/wiki/Lung_cancer
A uterine cancer that is located_in tissues lining the uterus.
DOID:5654
EFO:0004230
GARD:11981
ICD10CM:C54.1
KEGG:05213
MESH:D016889
NCI2004_11_17:C27815
NCI2004_11_17:C3012
NCI:C27815
NCI:C3012
OMIM:608089
UMLS_CUI:C0007103
UMLS_CUI:C0014170
endometrial Ca
endometrial neoplasm
malignant endometrial neoplasm
malignant neoplasm of endometrium
neoplasm of endometrium
primary malignant neoplasm of endometrium
tumor of Endometrium
disease_ontology
DOID:1380
endometrial cancer
A uterine cancer that is located_in tissues lining the uterus.
url:http://www.cancer.gov/dictionary?CdrID=444987
A large intestine cancer that is located_in the anus.
DOID:12240
GARD:9300
ICD10CM:C21.0
ICD10CM:C21.1
ICD9CM:154.2
ICD9CM:154.3
NCI2004_11_17:C7379
NCI:C7379
SNOMEDCT_US_2018_03_01:93669004
SNOMEDCT_US_2018_03_01:93676009
UMLS_CUI:C0153445
UMLS_CUI:C0153446
anal cancer
malignant anal tumor
disease_ontology
DOID:14110
anus cancer
A large intestine cancer that is located_in the anus.
url:http://en.wikipedia.org/wiki/Anus
ICD10CM:H31.9
ICD9CM:363.9
MESH:D015862
NCI:C34468
UMLS_CUI:C0008521
disease_ontology
DOID:1417
choroid disease
A urinary system disease that is located_in the ureter.
MESH:D014515
NCI:C27148
UMLS_CUI:C0041954
disease_ontology
DOID:1426
ureteral disease
A urinary system disease that is located_in the ureter.
url:http://www.nlm.nih.gov/medlineplus/ureteraldisorders.html
A disease that is characterized by abnormally rapid cell division.
DOID:0000818
cell process disease
neoplasm
disease_ontology
DOID:14566
disease of cellular proliferation
A disease that is characterized by abnormally rapid cell division.
url:http://en.wikipedia.org/w/index.php?title=Cell_proliferation
A sensory system disease that is located_in the eye or the adnexa of the eye.
ICD10CM:H35.00
ICD9CM:362.10
SNOMEDCT_US_2018_03_01:31411005
SNOMEDCT_US_2018_03_01:42873008
UMLS_CUI:C0004608
disease_ontology
DOID:1492
eye and adnexa disease
A sensory system disease that is located_in the eye or the adnexa of the eye.
url:http://en.wikipedia.org/wiki/Category:Diseases_of_the_eye_and_adnexa
A disease of anatomical entity that is located_in reproductive system organs.
DOID:6309
NCI:C27613
UMLS_CUI:C1335037
genital system disease
disease_ontology
DOID:15
reproductive system disease
A disease of anatomical entity that is located_in reproductive system organs.
url:http://en.wikipedia.org/wiki/Reproductive_system
A colon cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.
NCI2004_11_17:C4910
NCI:C4910
UMLS_CUI:C0699790
Colonic carcinoma
carcinoma of colon
disease_ontology
DOID:1520
OMIM mapping confirmed by DO. [SN].
colon carcinoma
A colon cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.
url:http://en.wikipedia.org/wiki/Carcinoma
A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm.
DOID:3226
ICD10CM:J96-J99
ICD10CM:J98
ICD9CM:510-519.99
ICD9CM:519
UMLS_CUI:C0029582
disease_ontology
DOID:1579
respiratory system disease
A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm.
url:http://en.wikipedia.org/wiki/File:Respiratory_system_complete_en.svg
url:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=respiratory%20system
A disease of anatomical entity that is located_in the integumentary system comprising the skin and its appendages.
disease_ontology
DOID:16
integumentary system disease
A disease of anatomical entity that is located_in the integumentary system comprising the skin and its appendages.
url:http://en.wikipedia.org/wiki/Integumentary_system
A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis.
ICD10CM:C80
ICD10CM:C80.1
ICD9CM:199
ICDO:M8000/3
MESH:D009369
NCI:C9305
SNOMEDCT_US_2018_03_01:38807002
UMLS_CUI:C0006826
malignant neoplasm
malignant tumor
primary cancer
disease_ontology
DOID:162
Updating out dated UMLS CUI.
cancer
A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis.
url:http://en.wikipedia.org/wiki/cancer
url:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=cancer
A disease of anatomical entity that occurs in the muscular and/or skeletal system.
MESH:D009140
NCI:C107377
SNOMEDCT_US_2018_03_01:928000
UMLS_CUI:C0026857
disease_ontology
DOID:17
musculoskeletal system disease
A disease of anatomical entity that occurs in the muscular and/or skeletal system.
url:http://en.wikipedia.org/wiki/Human_musculoskeletal_system#Diseases_and_disorders
An organ system cancer located_in endocrine system that is characterized by uncontrolled cellular proliferation of the hormone producing glands of the endocrine system.
DOID:10009
CSP2005:2009-5861
ICD10CM:C75.9
ICD9CM:194.9
MESH:D004701
NCI2004_11_17:C3010
NCI2004_11_17:C3575
NCI:C3010
NCI:C3575
SNOMEDCT_US_2018_03_01:93780007
UMLS_CUI:C0014132
UMLS_CUI:C0153658
Endocrine tumor
endocrine neoplasm
malignant Endocrine tumor
malignant neoplasm of endocrine gland
malignant tumour of endocrine gland
neoplasm of endocrine gland
neoplasm of endocrine system
disease_ontology
DOID:170
endocrine gland cancer
An organ system cancer located_in endocrine system that is characterized by uncontrolled cellular proliferation of the hormone producing glands of the endocrine system.
url:http://en.wikipedia.org/wiki/Endocrine_system
A cardiovascular cancer that is located_in blood vessels.
DOID:3339
DOID:5454
DOID:5548
DOID:7019
DOID:7020
DOID:7392
CSP2005:2007-0683
MESH:D019043
NCI2004_11_17:C5380
NCI2004_11_17:C5383
NCI2004_11_17:C5388
NCI2004_11_17:C7387
NCI2004_11_17:C7388
NCI2004_11_17:C7390
NCI:C5348
NCI:C5380
NCI:C5383
NCI:C5388
NCI:C7388
NCI:C7390
SNOMEDCT_US_2018_03_01:93817006
UMLS_CUI:C0282607
UMLS_CUI:C0346845
UMLS_CUI:C1290407
UMLS_CUI:C1334616
UMLS_CUI:C1334617
UMLS_CUI:C1334630
UMLS_CUI:C1335753
Blood Vessel neoplasm
Blood vessel tumor
Blood vessel tumors
Blood vessel tumour disorder
Haemangiomatous tumour
blood vessel neoplasm
leiomyosarcoma of the renal Vein
malignant great vessel tumor
malignant tumor of pulmonary Vein
malignant tumor of pulmonary artery
malignant vascular neoplasm
malignant vascular tumor
neoplasm of great vessel
pulmonary artery malignant neoplasm
pulmonary vein malignant neoplasm
renal vein leiomyosarcoma
vascular tissue neoplasm
vascular tumors
disease_ontology
DOID:175
vascular cancer
A cardiovascular cancer that is located_in blood vessels.
url:http://en.wikipedia.org/wiki/Vascular
An organ system cancer that located_in the heart and blood vessels.
CSP2005:2007-0683
NCI2004_11_17:C4784
NCI:C4784
UMLS_CUI:C0497243
Cardiovascular tumors
cardiovascular neoplasm
disease_ontology
DOID:176
cardiovascular cancer
An organ system cancer that located_in the heart and blood vessels.
url:http://www.cancer.gov/dictionary?CdrID=44005
url:http://www.healthcentral.com/heart-disease/h/cardiovascular-cancer.html
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.
DOID:0000405
DOID:2403
DOID:2869
DOID:324
DOID:325
DOID:45
ICD10CM:I72.9
ICD9CM:442.9
MESH:D000783
MESH:D014652
MESH:D020758
MESH:D020760
NCI:C26693
NCI:C35117
SNOMEDCT_US_2018_03_01:27550009
SNOMEDCT_US_2018_03_01:85659009
UMLS_CUI:C0002940
UMLS_CUI:C0042373
UMLS_CUI:C0752127
UMLS_CUI:C0752130
vascular tissue disease
disease_ontology
DOID:178
vascular disease
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.
url:http://en.wikipedia.org/wiki/Vascular_disease
A disease of anatomical entity that is located_in kidney, ureter, bladder and urethra.
DOID:579
NCI2004_11_17:C27599
NCI:C27599
UMLS_CUI:C1335051
Non-neoplastic urinary tract disease
urinary tract disease
disease_ontology
DOID:18
urinary system disease
A disease of anatomical entity that is located_in kidney, ureter, bladder and urethra.
url:http://en.wikipedia.org/wiki/Urinary_system
A connective tissue cancer that is located_in bone and is characterized by uncontrolled cellular proliferation that destroys normal bone tissue.
DOID:3348
CSP2005:2019-1041
MESH:D001859
NCI2004_11_17:C4016
NCI2004_11_17:C9343
NCI:C9343
UMLS_CUI:C0005967
CA - bone cancer
bone neoplasm
bone tumour
malignant bone neoplasm
malignant bone tumour
malignant neoplasm of bone
malignant osseous tumor
neoplasm of bone
osseous tumor
disease_ontology
DOID:184
bone cancer
A connective tissue cancer that is located_in bone and is characterized by uncontrolled cellular proliferation that destroys normal bone tissue.
url:http://www.cancer.gov/cancertopics/factsheet/Sites-Types/bone
url:http://www.cancer.gov/cancertopics/types/bone
url:http://www.wrongdiagnosis.com/b/bone_cancer/intro.htm
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.
MESH:D007573
UMLS_CUI:C0022364
neoplasm of jaw
disease_ontology
jaw neoplasm
DOID:1862
jaw cancer
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.
url:http://www.buzzle.com/articles/jaw-cancer-symptoms.html
MESH:D012888
NCI:C3375
UMLS_CUI:C0037305
disease_ontology
DOID:1863
skull cancer
An organ system cancer that is manifested in the reproductive organs.
DOID:1900
NCI2004_11_17:C3674
NCI:C3674
UMLS_CUI:C0178830
Reproductive tumor
malignant reproductive system neoplasm
disease_ontology
cancer of reproductive system
DOID:193
reproductive organ cancer
An organ system cancer that is manifested in the reproductive organs.
url:http://en.wikipedia.org/wiki/Reproductive_system#Examples_of_cancers
A female reproductive system disease that is located_in the fallopian tube.
MESH:D005184
NCI:C26771
UMLS_CUI:C0015556
disease_ontology
DOID:1962
fallopian tube disease
A female reproductive system disease that is located_in the fallopian tube.
url:https://www.ncbi.nlm.nih.gov/pubmed/21415195
A female reproductive organ cancer that is located_in fallopian tube.
DOID:1961
GARD:9162
ICD10CM:C57.0
ICD9CM:183.2
MESH:D005185
MTHICD9_2006:183.2
NCI2004_11_17:C3032
NCI2004_11_17:C7480
NCI:C3032
NCI:C7480
SNOMEDCT_US_2018_03_01:93794008
UMLS_CUI:C0015558
UMLS_CUI:C0153579
fallopian tube neoplasm
malignant neoplasm of uterine tube
malignant tumor of fallopian tube
malignant tumour of fallopian tube
neoplasm of fallopian tube
tumor of the fallopian tube
tumor, fallopian tube, malignant
disease_ontology
DOID:1964
fallopian tube cancer
A female reproductive organ cancer that is located_in fallopian tube.
url:http://en.wikipedia.org/wiki/Fallopian_tube_cancer
A colorectal cancer that is located_in the rectum.
DOID:1989
ICD10CM:C20
ICD9CM:154.1
MESH:D012004
NCI2004_11_17:C7418
NCI2004_11_17:C9382
NCI:C7418
NCI:C9382
SNOMEDCT_US_2018_03_01:93984006
UMLS_CUI:C0007113
UMLS_CUI:C0949022
carcinoma of rectum
carcinoma of the rectum
malignant Rectal tumor
malignant neoplasm of rectum
malignant rectum tumor
malignant tumor of rectum
rectal cancer
disease_ontology
cancer of rectum
DOID:1993
rectum cancer
A colorectal cancer that is located_in the rectum.
url:http://www.cancer.gov/dictionary?CdrID=529764
A musculoskeletal system cancer that is located_in connective tissue.
CSP2005:2008-3809
MESH:D009372
UMLS_CUI:C0027656
Tumour of connective tissue
connective tissue neoplasm
neoplasm of connective tissues
disease_ontology
DOID:201
connective tissue cancer
A musculoskeletal system cancer that is located_in connective tissue.
url:http://en.wikipedia.org/wiki/Connective_tissue
A sensory system cancer located_in the eye that is characterized by uncontrolled cellular proliferation in the eye.
DOID:9985
CSP2005:2018-3273
ICD9CM:190.8
MESH:D005134
NCI2004_11_17:C3030
NCI:C3030
UMLS_CUI:C0015414
UMLS_CUI:C0153632
Ocular tumor
eye neoplasm
malignant eye neoplasm
neoplasm of eye
neoplasm of eye proper
disease_ontology
DOID:2174
ocular cancer
A sensory system cancer located_in the eye that is characterized by uncontrolled cellular proliferation in the eye.
url:http://en.wikipedia.org/wiki/Eye
url:http://en.wikipedia.org/wiki/Eye_neoplasm
A colorectal cancer that is located_in the colon.
ICD10CM:C18
ICD10CM:C18.9
ICD9CM:153
ICD9CM:153.9
MESH:D003110
NCI:C9242
SNOMEDCT_US_2018_03_01:93761005
UMLS_CUI:C0007102
disease_ontology
DOID:219
colon cancer
A colorectal cancer that is located_in the colon.
url:http://www.cancer.gov/dictionary?CdrID=44237
A uterine disease that is located_in the cervix.
MESH:D002577
NCI:C40241
SNOMEDCT_US_2018_03_01:63339007
UMLS_CUI:C0007867
disease_ontology
DOID:2253
cervix disease
A uterine disease that is located_in the cervix.
url:https://www.mdedge.com/obgmanagement/article/136739/gynecology/2017-update-cervical-disease
An endocrine system disease that is located_in the gonads.
MESH:D006058
NCI:C26786
UMLS_CUI:C0018050
disease_ontology
DOID:2277
gonadal disease
An endocrine system disease that is located_in the gonads.
url:https://www.nature.com/subjects/gonadal-disorders
A reproductive system disease that impairs the ability to reproduce and is located in the uterus, vagina, cervix, ovaries or fallopian tubes.
ICD9CM:629.9
MESH:D005831
SNOMEDCT_US_2018_03_01:38233001
UMLS_CUI:C0017411
disease_ontology
DOID:229
female reproductive system disease
A reproductive system disease that impairs the ability to reproduce and is located in the uterus, vagina, cervix, ovaries or fallopian tubes.
url:http://en.wikipedia.org/wiki/Female_reproductive_system
url:http://en.wikipedia.org/wiki/Reproductive_system_disease
A colon carcinoma that derives_from epithelial cells of glandular origin.
NCI2004_11_17:C4349
NCI:C4349
UMLS_CUI:C0338106
Colonic adenocarcinoma
adenocarcinoma of colon
disease_ontology
adenocarcinoma of the colon
DOID:234
colon adenocarcinoma
colon adenocarcinoma
结肠腺癌
A colon carcinoma that derives_from epithelial cells of glandular origin.
url:http://en.wikipedia.org/wiki/Adenocarcinoma
ICD9CM:593.81
ICD9CM_2006:593.81
NCI:C35338
SNOMEDCT_US_2018_03_01:16934004
UMLS_CUI:C0268790
renal vascular disease
vascular disorder of kidney
disease_ontology
DOID:2388
renal artery disease
A female reproductive organ cancer that is located_in the ovary.
DOID:0060070
DOID:2144
DOID:9595
CSP2005:2016-1387
GARD:7295
ICD10CM:C56
ICD9CM:183.0
MESH:D010051
MTH:NOCODE
NCI2004_11_17:C4984
NCI2004_11_17:C7431
NCI:C4984
NCI:C7431
OMIM:167000
OMIM:607893
ORDO:213500
ORDO:213517
SNOMEDCT_US_2018_03_01:93934004
UMLS_CUI:C0919267
UMLS_CUI:C1140680
UMLS_CUI:C1299247
malignant Ovarian tumor
malignant tumour of ovary
ovarian neoplasm
ovary neoplasm
primary ovarian cancer
tumor of the Ovary
disease_ontology
DOID:2394
Xref MGI.
OMIM mapping confirmed by DO. [SN].
ovarian cancer
A female reproductive organ cancer that is located_in the ovary.
url:http://www.cancer.gov/dictionary?CdrID=445074
MESH:D007499
NCI:C34737
SNOMEDCT_US_2018_03_01:85478004
UMLS_CUI:C0022078
disease_ontology
DOID:240
iris disease
CSP2005:1114-7471
NCI:C35170
SNOMEDCT_US_2018_03_01:57534004
UMLS_CUI:C0154833
retina circulation disorder
disease_ontology
DOID:2462
retinal vascular disease
An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes.
DOID:1034
DOID:2532
CSP2005:2004-0139
MESH:D019337
NCI2004_11_17:C27134
NCI:C27134
UMLS_CUI:C0376544
Hematologic malignancy
Hematologic neoplasm
Hematological tumors
blood cancer
hematopoietic and lymphoid system tumor
hematopoietic cancer
hematopoietic neoplasm
hematopoietic tumors
malignant hematopoietic neoplasm
disease_ontology
DOID:2531
hematologic cancer
An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes.
url:http://en.wikipedia.org/wiki/Blood_cancer
url:http://www.cancer.gov/dictionary/?CdrID=45708
A urinary system cancer that is located_in the kidney.
DOID:11834
DOID:3676
ICD10CM:C64
ICD9CM:189.0
MESH:D007680
NCI:C120456
NCI:C3150
NCI:C7548
SNOMEDCT_US_2018_03_01:93849006
UMLS_CUI:C0022665
UMLS_CUI:C0494158
UMLS_CUI:C0740457
malignant neoplasm of kidney except pelvis
malignant tumour of kidney
renal cancer
disease_ontology
DOID:263
kidney cancer
A urinary system cancer that is located_in the kidney.
url:http://en.wikipedia.org/wiki/Kidney_cancer
NCI2004_11_17:C6531
NCI:C6531
UMLS_CUI:C1334624
malignant tumor of Synovium
disease_ontology
DOID:2706
synovium cancer
A disease of anatomical entity that is located_in endocrine glands which secretes a type of hormone directly into the bloodstream to regulate the body.
ICD10CM:E34.9
ICD9CM:259.9
MESH:D004700
NCI:C3009
SNOMEDCT_US_2018_03_01:67432001
UMLS_CUI:C0014130
disease_ontology
DOID:28
endocrine system disease
A disease of anatomical entity that is located_in endocrine glands which secretes a type of hormone directly into the bloodstream to regulate the body.
url:http://en.wikipedia.org/wiki/Endocrine_system
A female reproductive system disease characterized by the growth of endometrial tissue outside the uterine body.
EFO:0001065
ICD10CM:N80
ICD10CM:N80.9
ICD9CM:617
ICD9CM:617.9
MESH:D004715
NCI:C3014
SNOMEDCT_US_2018_03_01:11871002
UMLS_CUI:C0014175
disease_ontology
DOID:289
endometriosis
A female reproductive system disease characterized by the growth of endometrial tissue outside the uterine body.
url:https://en.wikipedia.org/?title=Endometriosis
url:https://www.ncbi.nlm.nih.gov/pubmed/20574791
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.
MTH:166
NCI2004_11_17:C9039
NCI:C9039
SNOMEDCT_US_2018_03_01:93752005
UMLS_CUI:C0302592
cancer of cervix
carcinoma OF CERVIX
carcinoma cervix uteri
carcinoma of cervix
carcinoma of the Cervix Uteri
disease_ontology
DOID:2893
OMIM mapping confirmed by DO. [SN].
cervix carcinoma
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.
url:http://en.wikipedia.org/wiki/Cervical_cancer
A carcinoma that has_material_basis_in abnormally proliferating cells, derives_from epithelial cells, which originate in glandular tissue.
MESH:D000230
NCI:C2852
SNOMEDCT_US_2018_03_01:35917007
UMLS_CUI:C0001418
adenocarcinomas
disease_ontology
DOID:299
adenocarcinoma
adenocarcinoma
腺癌
A carcinoma that has_material_basis_in abnormally proliferating cells, derives_from epithelial cells, which originate in glandular tissue.
url:http://en.wikipedia.org/wiki/Adenocarcinoma
An adenocarcinoma that derives_from epithelial cells originating in glandular tissue, which produce mucin.
DOID:4532
MESH:D002288
NCI2004_11_17:C26712
NCI2004_11_17:C27379
NCI2004_11_17:C27825
NCI:C26712
NCI:C27379
NCI:C27825
SNOMEDCT_US_2018_03_01:72495009
SNOMEDCT_US_2018_03_01:900006
UMLS_CUI:C0007130
UMLS_CUI:C0334368
Mucin-Secreting adenocarcinoma
Mucin-Secreting carcinoma
Mucin-producing adenocarcinoma
Mucous carcinoma
Pseudomyxoma peritonei with unknown primary site
mucin-producing adenocarcinoma
disease_ontology
DOID:3030
mucinous adenocarcinoma
An adenocarcinoma that derives_from epithelial cells originating in glandular tissue, which produce mucin.
url:http://coloncancer.about.com/od/typesofcancer/a/Mucinous_Tumor.htm
url:http://medical-dictionary.thefreedictionary.com/mucinous+carcinoma
A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.
DOID:2428
DOID:6570
CSP2005:2000-5801
MESH:D002277
MESH:D009375
NCI2004_11_17:C6927
NCI:C2916
NCI:C3709
SNOMEDCT_US_2018_03_01:68453008
SNOMEDCT_US_2018_03_01:71298006
UMLS_CUI:C0007097
UMLS_CUI:C0553707
UMLS_CUI:C1368683
epithelial cancer
epithelioma
malignant Epithelioma
disease_ontology
DOID:305
carcinoma
carcinoma
癌
A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.
url:http://en.wikipedia.org/wiki/Carcinoma
An organ system cancer located_in the nervous system that affects the central or peripheral nervous system.
DOID:1193
DOID:3195
DOID:4695
CSP2005:2012-5157
ICD9CM:192
ICD9CM:192.9
MESH:D009380
NCI2004_11_17:C3268
NCI2004_11_17:C35562
NCI:C35562
UMLS_CUI:C0027665
UMLS_CUI:C0153643
UMLS_CUI:C1334956
malignant neoplasm of nervous system
neoplasm of nervous system
nervous system neoplasm
neural neoplasm
neural tumor
tumor of the nervous system
disease_ontology
DOID:3093
nervous system cancer
An organ system cancer located_in the nervous system that affects the central or peripheral nervous system.
url:http://emedicine.medscape.com/oncology
url:http://en.wikipedia.org/wiki/Nervous_system_disease
An organ system cancer located_in gastrointestinal tract that is manifested in organs of the gastrointestinal system.
DOID:4945
DOID:8377
ICD10CM:C26.9
ICD9CM:239.0
MESH:D004067
MESH:D005770
NCI2004_11_17:C3052
NCI2004_11_17:C4890
NCI:C3052
NCI:C4890
SNOMEDCT_US_2018_03_01:93811007
UMLS_CUI:C0012243
UMLS_CUI:C0017185
UMLS_CUI:C0685938
GI tumor
digestive system cancer
gastrointestinal tract cancer
disease_ontology
DOID:3119
gastrointestinal system cancer
An organ system cancer located_in gastrointestinal tract that is manifested in organs of the gastrointestinal system.
url:http://en.wikipedia.org/wiki/Human_gastrointestinal_tract
DOID:11479
DOID:11993
MESH:D001004
MTHICD9_2006:565.0
NCI:C26695
SNOMEDCT_US_2018_03_01:32110003
UMLS_CUI:C0003462
Nontraumatic tear of anus
Solitary anal ulcer
Ulcer of anus
anal disease
anal fissure
anal fissure and fistula
anal ulcer
fissure in ano
disease_ontology
DOID:3128
anus disease
ICD10CM:G95.9
ICD9CM:336.9
MESH:D013118
NCI:C97110
SNOMEDCT_US_2018_03_01:48522003
SNOMEDCT_US_2018_03_01:95648003
UMLS_CUI:C0037928
disease_ontology
myelopathy
DOID:319
spinal cord disease
ICD10CM:S12.8
MESH:D014133
NCI:C35079
SNOMEDCT_US_2018_03_01:47125007
UMLS_CUI:C0040580
disease_ontology
DOID:3225
tracheal disease
A nervous system disease that affects either the spinal cord (myelopathy) or brain (encephalopathy) of the central nervous system.
ICD10CM:G96.9
MESH:D002493
NCI:C2934
SNOMEDCT_US_2018_03_01:23853001
UMLS_CUI:C0007682
disease_ontology
DOID:331
central nervous system disease
A nervous system disease that affects either the spinal cord (myelopathy) or brain (encephalopathy) of the central nervous system.
url:http://en.wikipedia.org/wiki/Central_nervous_system_disease
MESH:D002340
NCI:C84476
UMLS_CUI:C0007273
disorder of carotid artery
disease_ontology
DOID:3407
carotid artery disease
A female reproductive system disease that is located_in the uterus.
ICD10CM:N85.9
ICD9CM:621.9
MESH:D014591
NCI:C26907
SNOMEDCT_US_2018_03_01:12337004
UMLS_CUI:C0042131
disease_ontology
DOID:345
uterine disease
A female reproductive system disease that is located_in the uterus.
url:http://www.merriam-webster.com/dictionary/uterus
DOID:6353
MESH:D015811
NCI2004_11_17:C3142
NCI2004_11_17:C4554
NCI:C3142
NCI:C4554
UMLS_CUI:C0022079
UMLS_CUI:C0346372
malignant neoplasm of the Iris
malignant tumor of iris
tumor of the Iris
disease_ontology
DOID:3478
iris cancer
DOID:12754
MESH:D014604
NCI2004_11_17:C3436
NCI2004_11_17:C6105
NCI:C3436
NCI:C6105
UMLS_CUI:C0042162
UMLS_CUI:C1334629
Uveal tumor
malignant Uveal tumor
malignant uvea neoplasm
disease_ontology
DOID:3479
uveal cancer
An eye disease affecting the uvea, which are the pigmented layers of the eye consisting of the iris, ciliary body, and choroid.
GARD:8192
MESH:D014603
NCI:C26908
SNOMEDCT_US_2018_03_01:95678007
UMLS_CUI:C0042161
disease_ontology
DOID:3480
uveal disease
An eye disease affecting the uvea, which are the pigmented layers of the eye consisting of the iris, ciliary body, and choroid.
url:https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C26908
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.
DOID:2472
ICD10CM:L03.90
MESH:D002481
NCI:C26715
NCI:C34454
SNOMEDCT_US_2018_03_01:62837005
SNOMEDCT_US_2018_03_01:74276003
UMLS_CUI:C0007642
UMLS_CUI:C0007646
disease_ontology
DOID:3488
cellulitis
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.
url:http://en.wikipedia.org/wiki/Cellulitis
A nervous system cancer that is located_in the central nervous system.
DOID:0060093
DOID:1318
CSP2005:2012-5421
EFO:0000326
ICD10CM:C72.9
MESH:D016543
NCI2004_11_17:C4627
NCI2004_11_17:C9293
NCI:C4627
NCI:C9293
SNOMEDCT_US_2018_03_01:93744007
UMLS_CUI:C0085136
UMLS_CUI:C0348374
CNS neoplasm
central nervous system tumor
central nervous system tumors
malignant neoplasm of central nervous system
malignant tumor of CNS
neoplasm of central nervous system
disease_ontology
DOID:3620
central nervous system cancer
A nervous system cancer that is located_in the central nervous system.
url:http://en.wikipedia.org/wiki/Central_nervous_system
A female reproductive organ cancer that is located_in the uterus.
DOID:4363
CSP2005:2016-1566
ICD10CM:C55
ICD9CM:179
MESH:D014594
NCI2004_11_17:C3435
NCI2004_11_17:C3552
NCI:C3435
NCI:C3552
SNOMEDCT_US_2018_03_01:93718007
SNOMEDCT_US_2018_03_01:94127009
UMLS_CUI:C0042138
UMLS_CUI:C0153567
CA - cancer of uterus
Tumour of uterus
malignant neoplasm of uterus
malignant uterine tumor
neoplasm of uterus
uterine tumor
uterus neoplasm
disease_ontology
DOID:363
uterine cancer
A female reproductive organ cancer that is located_in the uterus.
url:http://www.cancer.gov/dictionary?CdrID=445094
A urinary system disease that is located_in the bladder.
ICD10CM:N32.9
ICD9CM:596.9
MESH:D001745
NCI:C2900
SNOMEDCT_US_2018_03_01:42643001
UMLS_CUI:C0005686
Urinary Bladder Disease
disease_ontology
DOID:365
bladder disease
A urinary system disease that is located_in the bladder.
url:http://www.nlm.nih.gov/medlineplus/bladderdiseases.html
An integumentary system disease that is located_in skin.
DOID:1576
DOID:1698
DOID:187
DOID:6486
DOID:8948
ICD9CM:702
MESH:D012871
MESH:D012873
NCI:C27554
NCI:C3371
SNOMEDCT_US_2018_03_01:5613003
SNOMEDCT_US_2018_03_01:80659006
SNOMEDCT_US_2018_03_01:95320005
UMLS_CUI:C0029574
UMLS_CUI:C0037274
UMLS_CUI:C0037277
Genodermatosis
skin and subcutaneous tissue disease
disease_ontology
DOID:37
skin disease
An integumentary system disease that is located_in skin.
url:http://en.wikipedia.org/wiki/Skin_disease
A cervix carcinoma that derives_from epithelial cells of glandular origin.
NCI2004_11_17:C4029
NCI:C4029
UMLS_CUI:C0279672
adenocarcinoma cervix uteri
adenocarcinoma of cervix
adenocarcinoma of the uterine Cervix
disease_ontology
DOID:3702
cervical adenocarcinoma
cervical adenocarcinoma
子宫颈腺癌
A cervix carcinoma that derives_from epithelial cells of glandular origin.
url:http://en.wikipedia.org/wiki/Adenocarcinoma
A stomach carcinoma that derives_from epithelial cells of glandular origin.
NCI2004_11_17:C4004
NCI:C4004
UMLS_CUI:C0278701
adenocarcinoma of stomach
stomach adenocarcinoma
disease_ontology
DOID:3717
gastric adenocarcinoma
gastric adenocarcinoma
胃腺癌
A stomach carcinoma that derives_from epithelial cells of glandular origin.
url:http://en.wikipedia.org/wiki/Adenocarcinoma
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.
EFO:0001071
ICD10CM:C34.90
NCI2004_11_17:C4878
NCI:C4878
UMLS_CUI:C0684249
cancer of lung
disease_ontology
carcinoma of lung
DOID:3905
OMIM mapping confirmed by DO. [SN].
lung carcinoma
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.
url:https://merck.com/mmpe/sec05/ch062/ch062b.html
A lung carcinoma that is characterized as any type of epithelial lung cancer other than small cell lung carcinoma.
EFO:0003060
KEGG:05223
MESH:D002289
NCI:C2926
UMLS_CUI:C0007131
NSCLC
Non-small cell lung cancer
non-small cell lung carcinoma
disease_ontology
DOID:3908
lung non-small cell carcinoma
non-small cell lung carcinoma
non-small cell lung carcinoma
非小细胞肺癌
A lung carcinoma that is characterized as any type of epithelial lung cancer other than small cell lung carcinoma.
url:http://en.wikipedia.org/wiki/Non-small-cell_lung_carcinoma
An organ system cancer that is located_in the kidneys, ureteres, bladder or urethra.
ICD10CM:C68.9
ICD9CM:189.9
UMLS_CUI:C0348371
disease_ontology
DOID:3996
urinary system cancer
An organ system cancer that is located_in the kidneys, ureteres, bladder or urethra.
url:http://en.wikipedia.org/wiki/Urinary_system
A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
MESH:D004194
NCI:C2991
SNOMEDCT_US_2018_03_01:64572001
UMLS_CUI:C0012634
disease_ontology
DOID:4
disease
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.
url:http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
A gastrointestinal system disease that is located_in the mouth.
MESH:D009059
NCI:C27641
NCI:C3240
UMLS_CUI:C0026636
disease_ontology
DOID:403
mouth disease
A gastrointestinal system disease that is located_in the mouth.
url:http://en.wikipedia.org/wiki/Oral_and_maxillofacial_pathology
NCI2004_11_17:C6516
NCI:C6516
UMLS_CUI:C1334619
malignant tumor of Skeletal Muscle
disease_ontology
DOID:4043
skeletal muscle cancer
A musculoskeletal system cancer that is located_in muscle.
DOID:4046
ICD10CM:C49
MESH:D009217
MESH:D019042
NCI2004_11_17:C4883
NCI:C4883
SNOMEDCT_US_2018_03_01:20667008
SNOMEDCT_US_2018_03_01:93913006
UMLS_CUI:C0027095
UMLS_CUI:C0684743
malignant neoplasm of muscle
malignant tumor of muscle
malignant tumor of the Muscle
myosarcoma
disease_ontology
DOID:4045
muscle cancer
A musculoskeletal system cancer that is located_in muscle.
url:http://en.wikipedia.org/wiki/Muscle
An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells.
GARD:10421
MESH:D012878
MTH:NOCODE
NCI2004_11_17:C2920
NCI:C2920
SNOMEDCT_US_2018_03_01:94047004
UMLS_CUI:C0007114
CA - skin cancer
malignant neoplasm of skin
melanoma and Non-melanoma skin cancer
disease_ontology
cancer of skin
DOID:4159
skin cancer
An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells.
url:http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0002414/
DOID:13974
DOID:4204
DOID:4208
GARD:8244
ICD10CM:C71.7
ICD9CM:191.7
MESH:D020295
NCI:C3570
NCI:C4869
NCI:C4975
NCI:C5967
SNOMEDCT_US_2018_03_01:93726004
UMLS_CUI:C0153641
UMLS_CUI:C0677866
UMLS_CUI:C0751886
UMLS_CUI:C1332192
malignant neoplasm of brain stem
malignant neoplasm of brainstem
neoplasm of adult brain stem
neoplasm of brain stem
primary brain Stem tumor
primary brain stem neoplasm
disease_ontology
DOID:4203
brain stem cancer
NCI2004_11_17:C6511
NCI:C6511
UMLS_CUI:C1334620
malignant tumor of Smooth Muscle
disease_ontology
DOID:4230
smooth muscle cancer
DOID:6352
ICD10CM:C69.4
NCI2004_11_17:C4364
NCI2004_11_17:C4766
NCI:C4364
NCI:C4766
SNOMEDCT_US_2018_03_01:93756008
UMLS_CUI:C0339349
UMLS_CUI:C0496833
malignant neoplasm of ciliary body
malignant tumor of ciliary body
malignant tumor of the Ciliary body
neoplasm of ciliary body
tumor of the Ciliary body
disease_ontology
DOID:4352
ciliary body cancer
NCI:C35775
SNOMEDCT_US_2018_03_01:68575007
UMLS_CUI:C0271100
disease_ontology
DOID:4353
ciliary body disease
A female reproductive organ cancer that is located_in the cervix.
DOID:4361
CSP2005:2016-1746
ICD10CM:C53
ICD10CM:C53.9
ICD9CM:180
ICD9CM:180.9
MESH:D002583
NCI2004_11_17:C2940
NCI:C2940
NCI:C9311
OMIM:603956
SNOMEDCT_US_2018_03_01:93752005
UMLS_CUI:C0007847
UMLS_CUI:C0007873
cervical neoplasm
cervix cancer
cervix uteri cancer
neoplasm of uterine cervix
tumor of the Cervix Uteri
uterine cervical neoplasm
disease_ontology
DOID:4362
cervical cancer
A female reproductive organ cancer that is located_in the cervix.
url:http://cancergenome.nih.gov/cancersselected/cervicalcancer
url:http://en.wikipedia.org/wiki/Cervical_cancer
url:http://www.cancer.gov/dictionary?CdrID=444973
DOID:770
ICD10CM:C69.2
ICD9CM:190.5
MESH:D019572
NCI2004_11_17:C3216
NCI2004_11_17:C4800
NCI:C3216
NCI:C4800
SNOMEDCT_US_2018_03_01:93987004
UMLS_CUI:C0024622
UMLS_CUI:C0524801
Retinal tumor
malignant Retinal neoplasm
malignant neoplasm of retina
malignant tumor of retina
neoplasm of retina
disease_ontology
DOID:4645
retinal cancer
A brain cancer that is located_in the infratentorial region.
DOID:4789
ICD10CM:C71.7
MESH:D015192
NCI2004_11_17:C3139
NCI2004_11_17:C4966
NCI:C3139
NCI:C4966
UMLS_CUI:C0021432
UMLS_CUI:C0751593
brain neoplasm, Infratentorial
malignant Infratentorial tumors
disease_ontology
DOID:4706
infratentorial cancer
A brain cancer that is located_in the infratentorial region.
url:http://en.wikipedia.org/wiki/Tentorium_cerebelli
url:http://www.ncbi.nlm.nih.gov/mesh/68015192
DOID:12343
ICD10CM:C65
ICD9CM:189.1
NCI2004_11_17:C6142
NCI2004_11_17:C7525
NCI:C6142
NCI:C7525
SNOMEDCT_US_2018_03_01:93985007
UMLS_CUI:C0153618
UMLS_CUI:C1335749
carcinoma of kidney Pelvis
malignant neoplasm of renal pelvis
malignant renal Pelvis neoplasm
malignant tumor of renal pelvis
renal pelvis cancer
disease_ontology
DOID:4919
renal pelvis carcinoma
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.
DOID:3937
CSP2005:2005-5041
ICD10CM:C76.1
ICD9CM:195.1
MESH:D013899
NCI2004_11_17:C3406
NCI:C3406
NCI:C3576
UMLS_CUI:C0039981
UMLS_CUI:C0153661
Thoracic tumor
thorax cancer
thorax neoplasm
tumor of thorax
disease_ontology
DOID:5093
thoracic cancer
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.
url:http://www.advocatehealth.com/cmc/body.cfm?id=203
An artery disease that is characterized by degeneration of the cells composing the aortic wall.
CSP2005:0571-0627
MESH:D001018
NCI:C101253
SNOMEDCT_US_2018_03_01:47040006
UMLS_CUI:C0003493
aortic disorder
disorder of the aorta
disease_ontology
DOID:520
aortic disease
An artery disease that is characterized by degeneration of the cells composing the aortic wall.
url:http://www.hopkinsmedicine.org/heart_vascular_institute/conditions_treatments/conditions/aorta.html
NCI2004_11_17:C4574
NCI:C4574
UMLS_CUI:C0346811
malignant neoplasm of Dermis
malignant tumor of dermis
disease_ontology
DOID:5274
malignant dermis tumor
A gastrointestinal system disease that is located_in the intestine.
DOID:10759
DOID:11222
DOID:11789
DOID:8531
DOID:8558
DOID:8591
ICD10CM:K63.9
ICD9CM:569.9
MESH:D007410
NCI:C26801
SNOMEDCT_US_2018_03_01:85919009
UMLS_CUI:C0021831
disease_ontology
DOID:5295
intestinal disease
A gastrointestinal system disease that is located_in the intestine.
url:http://en.wikipedia.org/wiki/Human_gastrointestinal_tract
DOID:10758
CSP2005:1248-3971
MESH:D003108
UMLS_CUI:C0009373
colon disorder
disease_ontology
DOID:5353
colonic disease
A stomach cancer that is located_in the stomach.
EFO:0000178
NCI2004_11_17:C4911
NCI:C4911
UMLS_CUI:C0699791
cancer of the stomach
carcinoma of stomach
gastric carcinoma
disease_ontology
DOID:5517
stomach carcinoma
A stomach cancer that is located_in the stomach.
url:http://en.wikipedia.org/wiki/Stomach_cancer
A urinary system disease that is located_in the kidney.
EFO:0003086
ICD10CM:N08
ICD10CM:N28.9
MESH:D007674
NCI:C3149
NCI:C34843
SNOMEDCT_US_2018_03_01:90708001
UMLS_CUI:C0022658
nephropathy
disease_ontology
DOID:557
kidney disease
A urinary system disease that is located_in the kidney.
url:http://www.nlm.nih.gov/medlineplus/kidneydiseases.html
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).
DOID:3638
DOID:7225
ICD10CM:C72.0
ICD9CM:192.2
MESH:D013120
MESH:D013125
NCI2004_11_17:C3381
NCI2004_11_17:C3382
NCI2004_11_17:C3572
NCI:C3381
NCI:C3572
SNOMEDCT_US_2018_03_01:94068003
UMLS_CUI:C0037930
UMLS_CUI:C0037939
UMLS_CUI:C0153646
Intraspinal tumor
malignant tumor of the Spinal Cord
spinal cord cancer
spinal cord neoplasm
tumor of the Spinal Cord
disease_ontology
spinal neoplasm
DOID:5612
spinal cancer
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).
url:http://en.wikipedia.org/wiki/Spinal_tumor
An eye and adnexa disease that is located_in the eye.
DOID:2933
ICD10CM:H44
ICD10CM:H44.9
ICD9CM:360
ICD9CM:360.9
ICD9CM:379.90
MESH:D005128
NCI:C26767
SNOMEDCT_US_2018_03_01:79517001
UMLS_CUI:C0015397
disease_ontology
DOID:5614
eye disease
An eye and adnexa disease that is located_in the eye.
url:http://en.wikipedia.org/wiki/Eye_disease
An intestinal cancer that effects the long, tube-like organ that is connected to the small intestine at one end and the anus at the other.
DOID:1994
DOID:1997
ICD10CM:C18.9
MESH:D015179
NCI:C2955
NCI:C4978
NCI:C5105
SNOMEDCT_US_2018_03_01:93854002
UMLS_CUI:C0009402
UMLS_CUI:C0346629
UMLS_CUI:C1319315
disease_ontology
DOID:5672
large intestine cancer
An 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.
url:http://en.wikipedia.org/wiki/Large_intestine
An eye disease that is located_in the retina.
ICD10CM:H35.9
ICD9CM:362.9
MESH:D012164
NCI:C26875
NCI:C62601
SNOMEDCT_US_2018_03_01:29555009
SNOMEDCT_US_2018_03_01:35426003
UMLS_CUI:C0035309
disease_ontology
DOID:5679
retinal disease
An eye disease that is located_in the retina.
url:http://en.wikipedia.org/wiki/Retina#Diseases_and_disorders
A nervous system disease that affects the peripheral nervous system.
DOID:13069
CSP2005:2042-6617
ICD10CM:G64
ICD9CM:350-359.99
MESH:D010523
MTH:516
NCI:C119734
NCI:C27580
NCI:C27587
SNOMEDCT_US_2018_03_01:42658009
UMLS_CUI:C0031117
UMLS_CUI:C1335029
disease_ontology
peripheral nerve disease
peripheral neuropathy
DOID:574
peripheral nervous system disease
A nervous system disease that affects the peripheral nervous system.
url:http://en.wikipedia.org/w/index.php?title=Peripheral_neuropathy&redirect=no
peripheral nerve disease
MTH:516
A hematologic cancer and central nervous system neoplasm that is located_in the central nervous system.
NCI2004_11_17:C5503
NCI:C5503
UMLS_CUI:C1332882
CNS hematopoietic tumor
disease_ontology
hematopoietic neoplasm of central nervous system
DOID:5772
central nervous system hematologic cancer
A hematologic cancer and central nervous system neoplasm that is located_in the central nervous system.
url:http://www.oncologystat.com/journals/ew/YSONC/Central_Nervous_System_Disease_in_Hematologic_Malignancies_Historical_Perspective_and_Practical_Applications.html
DOID:14538
NCI2004_11_17:C4570
NCI:C4570
NCI:C5346
SNOMEDCT_US_2018_03_01:93778001
UMLS_CUI:C0346612
UMLS_CUI:C1290401
malignant Endocardial tumor
malignant neoplasm of endocardium
malignant tumor of endocardium
disease_ontology
DOID:5877
endocardium cancer
An artery disease that is located in the lungs.
disease_ontology
DOID:60001
pulmonary artery disease
An artery disease that is located in the lungs.
url:https://www.ncbi.nlm.nih.gov/pubmed/23737196
DOID:12757
ICD10CM:C69.1
ICD9CM:190.4
NCI2004_11_17:C3565
NCI2004_11_17:C4361
NCI:C3565
NCI:C4361
SNOMEDCT_US_2018_03_01:93766000
UMLS_CUI:C0153629
UMLS_CUI:C0339304
Corneal tumor
malignant Corneal tumor
malignant neoplasm of cornea
malignant tumor of cornea
neoplasm of cornea
disease_ontology
DOID:6199
cornea cancer
A musculoskeletal system disease that affects tissues such as skin, tendons, and cartilage.
CSP2005:0729-7208
MESH:D003240
NCI:C26729
UMLS_CUI:C0009782
connective tissue disorder
disorder of connective tissue
disease_ontology
DOID:65
connective tissue disease
A musculoskeletal system disease that affects tissues such as skin, tendons, and cartilage.
url:http://www.niams.nih.gov/Health_Info/Scleroderma/default.asp
An vascular disease that is characterized by dysfunction of the blood vessels supplying the brain.
DOID:12214
DOID:3455
DOID:8231
CSP2005:0617-5539
EFO:0000712
ICD10CM:I60-I69
ICD10CM:I63.9
ICD10CM:I67.9
ICD9CM:430-438.99
ICD9CM:437.9
MESH:D002561
MESH:D020521
NCI:C2938
NCI:C3390
SNOMEDCT_US_2018_03_01:62914000
SNOMEDCT_US_2018_03_01:82797006
UMLS_CUI:C0007820
UMLS_CUI:C0038454
CVA
Cerebrovascular accident
cerebrovascular accident
cerebrovascular disorder
stroke
disease_ontology
DOID:6713
OMIM mapping confirmed by DO. [SN].
cerebrovascular disease
An vascular disease that is characterized by dysfunction of the blood vessels supplying the brain.
url:http://en.wikipedia.org/wiki/Cerebrovascular_disease
url:http://www.ncbi.nlm.nih.gov/books/NBK378/
A disease that manifests in a defined anatomical structure.
DOID:1
DOID:2
DOID:5
DOID:71
DOID:72
DOID:8
disease_ontology
DOID:7
disease of anatomical entity
A disease that manifests in a defined anatomical structure.
url:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=anatomic
A urinary system disease that is located_in the urethra.
ICD10CM:N36.9
MESH:D014522
NCI2004_11_17:C26903
NCI:C26903
SNOMEDCT_US_2018_03_01:4985009
UMLS_CUI:C0041969
urethra disease
disease_ontology
DOID:732
urethral disease
A urinary system disease that is located_in the urethra.
url:http://www.nlm.nih.gov/medlineplus/urethraldisorders.html
An urinary tract cancer that derives_from the tissues of the urethra.
DOID:737
GARD:9390
ICD10CM:C68.0
ICD9CM:189.3
MESH:D014523
NCI2004_11_17:C7507
NCI:C7507
NCI:C9106
SNOMEDCT_US_2018_03_01:94123008
UMLS_CUI:C0153620
UMLS_CUI:C0700101
malignant tumour of urethra
malignant urethral neoplasm
urethral Ca
disease_ontology
cancer of urethra
DOID:734
urethra cancer
An urinary tract cancer that derives_from the tissues of the urethra.
url:http://www.cancer.gov/cancertopics/pdq/treatment/urethral/Patient
A disease of anatomical entity that has_material_basis_in hematopoietic cells.
CSP2005:0427-3600
ICD10CM:D75.9
ICD9CM:280-289.99
ICD9CM:289.9
ICD9CM_2006:280-289.99
MESH:D006402
MTH:NOCODE
MTHICD9_2006:289.9
NCI:C26323
SNOMEDCT_US_2018_03_01:34093004
UMLS_CUI:C0018939
Blood disease
Blood dyscrasia
DISEASE OF THE BLOOD AND BLOOD-FORMING ORGANS
Hematological disease
blood disorder
disease of hematopoietic system
disease_ontology
DOID:74
hematopoietic system disease
A disease of anatomical entity that has_material_basis_in hematopoietic cells.
url:http://en.wikipedia.org/wiki/Hematopathology
url:https://www.ncbi.nlm.nih.gov/books/NBK1741/
A gastrointestinal system disease that is located_in the stomach.
MESH:D013272
NCI2004_11_17:C26886
NCI:C26886
SNOMEDCT_US_2018_03_01:29384001
UMLS_CUI:C0038354
Gastropathy
stomach disorder
disease_ontology
gastric disease
DOID:76
stomach disease
A gastrointestinal system disease that is located_in the stomach.
url:http://en.wikipedia.org/wiki/Stomach_disease
A disease of anatomical entity that is located_in the gastrointestinal tract.
DOID:27
DOID:944
CSP2005:1248-3545
ICD10CM:K92.9
ICD9CM:520-579.99
MESH:D004066
SNOMEDCT_US_2018_03_01:53619000
UMLS_CUI:C0012242
GIT disease
Gastroenteropathy
alimentary system disease
digestive system disorder
gastrointestinal disease
gastrointestinal disorder
disease_ontology
DOID:77
gastrointestinal system disease
A disease of anatomical entity that is located_in the gastrointestinal tract.
url:http://en.wikipedia.org/wiki/Human_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.
DOID:11894
DOID:11895
DOID:29
DOID:766
ICD10CM:J98.4
MESH:D008171
NCI:C3198
SNOMEDCT_US_2018_03_01:19829001
UMLS_CUI:C0024115
disease_ontology
DOID:850
Updating out dated CUI and removing lung abscess as a synonym.
lung disease
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.
url:http://www.niehs.nih.gov/health/topics/conditions/lung-disease/index.cfm
url:http://www.nlm.nih.gov/medlineplus/ency/article/000066.htm
A myeloid leukemia that is characterized by a dominance of monocytes in the marrow.
DOID:8526
DOID:8809
DOID:8884
DOID:8935
DOID:9151
CSP2005:2004-2820
ICD10CM:C93
ICD9CM:206.8
UMLS_CUI:C0153903
Schilling's leukemia
disease_ontology
DOID:8527
monocytic leukemia
A myeloid leukemia that is characterized by a dominance of monocytes in the marrow.
url:https://en.wikipedia.org/wiki/Monocytic_leukemia
DOID:8563
DOID:8605
DOID:8975
DOID:9031
DOID:9135
ICD10CM:C00
ICD10CM:C00.9
ICD9CM:140
ICD9CM:140.6
ICD9CM:140.8
MESH:D008048
MTHICD9_2006:140.4
MTHICD9_2006:140.5
MTHICD9_2006:140.6
MTHICD9_2006:140.9
NCI2004_11_17:C7485
NCI:C7485
SNOMEDCT_US_2018_03_01:93762003
SNOMEDCT_US_2018_03_01:93869001
UMLS_CUI:C0153340
UMLS_CUI:C0153346
UMLS_CUI:C0153347
malignant neoplasm of commissure of lip
malignant neoplasm of external Lip, not specified as upper or lower
malignant neoplasm of labial commissure of lip
malignant neoplasm of lip
malignant neoplasm of lip, external
malignant neoplasm of lip, inner aspect
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, mucosa
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
malignant tumor of commissure of lip
malignant tumor of labial mucosa
malignant tumor of lip
malignant tumor of lower labial mucosa
malignant tumor of the Lip
malignant tumour of labial commissure
malignant tumour of lip
disease_ontology
DOID:8564
lip cancer
A gastrointestinal system cancer that is located_in the oral cavity.
DOID:0050627
DOID:8617
DOID:9049
DOID:9055
GARD:9360
ICD10CM:C04
ICD10CM:C04.0
ICD10CM:C04.1
ICD10CM:C04.9
ICD9CM:144
ICD9CM:144.0
ICD9CM:144.1
ICD9CM:144.9
MTH:NOCODE
MTH:U001372
NCI2004_11_17:C9318
NCI:C9318
SNOMEDCT_US_2018_03_01:93672006
SNOMEDCT_US_2018_03_01:93802007
SNOMEDCT_US_2018_03_01:93860002
UMLS_CUI:C0153368
UMLS_CUI:C0153369
UMLS_CUI:C0496758
malignant neoplasm of anterior portion of floor of mouth
malignant neoplasm 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
disease_ontology
DOID:8618
oral cavity cancer
A gastrointestinal system cancer that is located_in the oral cavity.
url:http://en.wikipedia.org/wiki/Oral_cancer
A disease of anatomical entity that is located_in the central nervous system or located_in the peripheral nervous system.
ICD10CM:G00-G99
ICD10CM:G98
ICD10CM:G98.8
ICD9CM:349.9
MESH:D009422
NCI:C26835
UMLS_CUI:C0027765
disease_ontology
DOID:863
nervous system disease
A disease of anatomical entity that is located_in the central nervous system or located_in the peripheral nervous system.
url:http://en.wikipedia.org/wiki/Nervous_system
A vascular disease that is located_in a vein.
ICD10CM:I82
ICD9CM:453
UMLS_CUI:C0155774
disease_ontology
DOID:866
vein disease
A vascular disease that is located_in a vein.
url:http://en.wikipedia.org/wiki/Vein#Venous_diseases
A leukemia that is located_in myeloid tissue.
DOID:8878
DOID:8879
DOID:8910
DOID:9066
DOID:9126
CSP2005:2004-4431
GARD:8226
ICD10CM:C92
ICD10CM:C92.9
ICD10CM:C92.90
ICD9CM:205
ICD9CM:205.9
MESH:D007951
MTH:NOCODE
NCI2004_11_17:C3172
NCI:C3172
SNOMEDCT_US_2018_03_01:37810007
SNOMEDCT_US_2018_03_01:94717009
UMLS_CUI:C0023470
Non-Lymphocytic Leukemia
leukemia myelogenous
myeloid granulocytic leukemia
disease_ontology
DOID:8692
myeloid leukemia
A leukemia that is located_in myeloid tissue.
url:http://en.wikipedia.org/wiki/Myeloid_leukemia
A monocytic leukemia where the majority of monocytic cells are promonocytes.
DOID:9208
GARD:525
ICD9CM:206.0
MESH:D007948
NCI2004_11_17:C7318
OMIM:151380
SNOMEDCT_US_2018_03_01:22331004
SNOMEDCT_US_2018_03_01:91859000
UMLS_CUI:C0023465
acute Monoblastic Leukemia and acute Monocytic Leukemia
acute monocytic leukemia without mention of remission
acute monocytic leukemia, FAB M5
acute monocytic leukemia, morphology
disease_ontology
DOID:8864
OMIM mapping confirmed by DO. [SN].
acute monocytic leukemia
acute monocytic leukemia
急性单核细胞性白血病
A monocytic leukemia where the majority of monocytic cells are promonocytes.
url:https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=18.09d&ns=ncit&code=C4861
ICD10CM:C00.1
ICD9CM:140.1
SNOMEDCT_US_2018_03_01:94136008
UMLS_CUI:C0432520
disease_ontology
DOID:8883
lower lip cancer
A large intestine cancer that is located_in the colon and/or located_in the rectum.
KEGG:05210
MESH:D015179
OMIM:114500
UMLS_CUI:C1527249
disease_ontology
DOID:9256
Xref MGI.
OMIM mapping confirmed by DO. [SN].
colorectal cancer
A large intestine cancer that is located_in the colon and/or located_in the rectum.
url:http://www.cancer.gov/dictionary?CdrID=444983
ICD10CM:K13.0
ICD9CM:528.5
ICD9CM_2006:528.5
MESH:D008047
NCI:C26818
SNOMEDCT_US_2018_03_01:90678009
UMLS_CUI:C0023760
disease of lips
disease_ontology
DOID:9297
lip disease
DOID:14536
NCI2004_11_17:C4569
NCI2004_11_17:C5349
NCI:C4569
NCI:C5349
SNOMEDCT_US_2018_03_01:93914000
UMLS_CUI:C0346611
UMLS_CUI:C1290402
malignant Myocardial tumor
malignant neoplasm of myocardium
tumor of Myocardium
disease_ontology
DOID:9299
myocardium cancer
An adnexa disease that is located_in the eye socket.
ICD10CM:H05
ICD10CM:H05.9
ICD9CM:376
ICD9CM:376.9
MESH:D009916
SNOMEDCT_US_2018_03_01:11270005
UMLS_CUI:C0029182
disease_ontology
DOID:930
orbital disease
An adnexa disease that is located_in the eye socket.
url:http://www.hopkinsmedicine.org/wilmer/services/oculofacial_plastic_surgery/reconstructive/orbital_disease.html
A central nervous system disease that is located_in the brain.
DOID:8510
ICD10CM:G93.40
ICD10CM:G93.9
ICD9CM:348.3
ICD9CM:348.30
ICD9CM:348.9
MESH:D001927
NCI:C26920
NCI:C96413
SNOMEDCT_US_2018_03_01:76011009
SNOMEDCT_US_2018_03_01:81308009
UMLS_CUI:C0006111
UMLS_CUI:C0085584
encephalopathy
disease_ontology
DOID:936
brain disease
A central nervous system disease that is located_in the brain.
url:https://medlineplus.gov/braindiseases.html
A hematopoietic system disease that is located_in white blood cells.
ICD10CM:D72.9
ICD9CM:288
ICD9CM:288.9
MESH:D007960
SNOMEDCT_US_2018_03_01:54097007
UMLS_CUI:C0023510
disease_ontology
DOID:9500
leukocyte disease
A hematopoietic system disease that is located_in white blood cells.
url:https://rarediseases.org/rare-diseases/leukocyte-adhesion-deficiency-syndromes/
A respiratory system disease which involves the upper respiratory tract.
ICD9CM:478.1
ICD9CM:478.19
UMLS_CUI:C0029581
disease_ontology
DOID:974
upper respiratory tract disease
A respiratory system disease which involves the upper respiratory tract.
url:http://en.wikipedia.org/wiki/Category:Upper_respiratory_tract_diseases
url:http://www.who.int/topics/respiratory_tract_diseases/en/
Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
Wikipedia:Immune_system
biological_process
GO:0002376
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.
immune system process
Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
GOC:add
GOC:mtg_15nov05
GO_REF:0000022
Any process that modulates the frequency, rate, or extent of an immune system process.
biological_process
GO:0002682
regulation of immune system process
Any process that modulates the frequency, rate, or extent of an immune system process.
GOC:add
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
downregulation of immune system process
inhibition of immune system process
biological_process
GO:0002683
negative regulation of immune system process
Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune system process.
GOC:add
Any process that activates or increases the frequency, rate, or extent of an immune system process.
up regulation of immune system process
up-regulation of immune system process
upregulation of immune system process
activation of immune system process
stimulation of immune system process
biological_process
GO:0002684
positive regulation of immune system process
Any process that activates or increases the frequency, rate, or extent of an immune system process.
GOC:add
molecular_function
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.
molecular process
GO:0005554
molecular function
molecular_function
GO:0003674
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.
GO:molecular_function
molecular_function
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.
GOC:pdt
catalytic activity
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.
Wikipedia:Enzyme
enzyme activity
molecular_function
GO:0003824
catalytic activity
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.
GOC:vw
ISBN:0198506732
enzyme activity
GOC:dph
GOC:tb
true
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.
receptor binding
Wikipedia:Ligand_(biochemistry)
receptor ligand
molecular_function
receptor-associated protein activity
GO:0005102
Where appropriate, also consider annotating to 'receptor agonist activity ; GO:0048018'.
signaling receptor binding
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.
GOC:bf
GOC:ceb
ISBN:0198506732
The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule.
Wikipedia:Binding_(molecular)
ligand
molecular_function
GO:0005488
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.
binding
The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule.
GOC:ceb
GOC:mah
ISBN:0198506732
Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
GO:0001948
GO:0045308
MIPS_funcat:16.01
MIPS_funcat:18.01.07
Reactome:R-HSA-170835
Reactome:R-HSA-170846
protein amino acid binding
glycoprotein binding
molecular_function
GO:0005515
protein binding
Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
GOC:go_curators
Reactome:R-HSA-170835
An anchoring protein, ZFYVE9 (SARA), recruits SMAD2/3
Reactome:R-HSA-170846
TGFBR2 recruits TGFBR1
The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4).
phosphorus metabolism
biological_process
GO:0006793
phosphorus metabolic process
The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4).
GOC:ai
The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.
MIPS_funcat:01.04
phosphate metabolism
biological_process
phosphate metabolic process
GO:0006796
phosphate-containing compound metabolic process
The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.
GOC:ai
immune response
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
MIPS_funcat:36.25.16
biological_process
GO:0006955
This term was improved by GO_REF:0000022. It was redefined and moved.
immune response
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
GOC:add
GOC:mtg_15nov05
GO_REF:0000022
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.
Wikipedia:Cell_signaling
biological_process
GO:0007154
cell communication
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.
GOC:mah
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.
GO:0023033
MIPS_funcat:30
Wikipedia:Signal_transduction
signaling cascade
signalling cascade
biological_process
signaling pathway
signalling pathway
GO:0007165
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.
signal transduction
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.
GOC:go_curators
GOC:mtg_signaling_feb11
signalling pathway
GOC:mah
biological_process
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
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.
janelomax
2012-09-19T15:05:24Z
GO:0000004
GO:0007582
GO:0044699
Wikipedia:Biological_process
biological process
physiological process
biological_process
single organism process
single-organism process
GO:0008150
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this.
biological_process
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.
GOC:pdt
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.
janelomax
2012-10-17T15:46:40Z
GO:0044236
GO:0044710
MIPS_funcat:01
Wikipedia:Metabolism
metabolism
metabolic process resulting in cell growth
metabolism resulting in cell growth
multicellular organism metabolic process
biological_process
single-organism metabolic process
GO:0008152
Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
metabolic process
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.
GOC:go_curators
ISBN:0198547684
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
GO:0044252
down regulation of metabolic process
down-regulation of metabolic process
downregulation of metabolic process
negative regulation of metabolism
negative regulation of organismal metabolism
inhibition of metabolic process
inhibition of organismal metabolic process
negative regulation of multicellular organismal metabolic process
biological_process
GO:0009892
negative regulation of metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
GOC:go_curators
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
GO:0044253
positive regulation of metabolism
up regulation of metabolic process
up-regulation of metabolic process
upregulation of metabolic process
activation of metabolic process
positive regulation of multicellular organismal metabolic process
positive regulation of organismal metabolism
stimulation of metabolic process
stimulation of organismal metabolic process
up-regulation of organismal metabolic process
biological_process
GO:0009893
positive 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.
GOC:go_curators
Any process that modulates the frequency, rate or extent of signal transduction.
GO:0035466
biological_process
regulation of signaling pathway
regulation of signalling pathway
GO:0009966
regulation of signal transduction
Any process that modulates the frequency, rate or extent of signal transduction.
GOC:sm
regulation of signalling pathway
GOC:mah
Any process that activates or increases the frequency, rate or extent of signal transduction.
GO:0035468
up regulation of signal transduction
up-regulation of signal transduction
upregulation of signal transduction
activation of signal transduction
stimulation of signal transduction
biological_process
positive regulation of signaling pathway
positive regulation of signalling pathway
GO:0009967
positive regulation of signal transduction
Any process that activates or increases the frequency, rate or extent of signal transduction.
GOC:sm
positive regulation of signalling pathway
GOC:mah
Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction.
GO:0035467
down regulation of signal transduction
down-regulation of signal transduction
downregulation of signal transduction
inhibition of signal transduction
biological_process
negative regulation of signaling pathway
negative regulation of signalling pathway
GO:0009968
negative regulation of signal transduction
Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction.
GOC:sm
negative regulation of signalling pathway
GOC:mah
cellular process
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.
janelomax
2012-12-11T16:56:55Z
GO:0008151
GO:0044763
GO:0050875
cell physiology
cellular physiological process
cell growth and/or maintenance
biological_process
single-organism cellular process
GO:0009987
cellular process
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.
GOC:go_curators
GOC:isa_complete
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 receptor activity
biological_process
GO:0010469
regulation of signaling receptor activity
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.
GOC:dph
GOC:tb
Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
biological_process
GO:0010562
positive regulation of phosphorus metabolic process
Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
GOC:dph
GOC:tb
Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
biological_process
GO:0010563
negative 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.
GOC:dph
GOC:tb
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.
biological_process
GO:0010646
regulation of cell communication
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.
GOC:dph
GOC:tb
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.
biological_process
GO:0010647
positive regulation of cell communication
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.
GOC:dph
GOC:tb
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.
biological_process
GO:0010648
negative 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.
GOC:dph
GOC:tb
true
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Reactome:R-HSA-6788855
Reactome:R-HSA-6788867
phosphokinase activity
molecular_function
GO:0016301
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.
kinase activity
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
ISBN:0198506732
Reactome:R-HSA-6788855
FN3KRP phosphorylates PsiAm, RibAm
Reactome:R-HSA-6788867
FN3K phosphorylates ketosamines
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.
Wikipedia:Phosphorylation
biological_process
GO:0016310
phosphorylation
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.
ISBN:0198506732
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.
EC:2
Reactome:R-HSA-1483089
Reactome:R-HSA-1483186
Reactome:R-HSA-5668414
Reactome:R-HSA-6787403
Reactome:R-HSA-8868783
molecular_function
GO:0016740
transferase activity
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.
ISBN:0198506732
Reactome:R-HSA-1483089
PE is converted to PS by PTDSS2
Reactome:R-HSA-1483186
PC is converted to PS by PTDSS1
Reactome:R-HSA-5668414
TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK
Reactome:R-HSA-6787403
GTPBP3 and MTO1 transform uridine-34 yielding 5-taurinomethyluridine-34 in tRNA
Reactome:R-HSA-8868783
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).
EC:2.7
molecular_function
GO:0016772
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
Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
GOC:jl
ISBN:0198506732
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
regulation of phosphate metabolism
biological_process
GO:0019220
regulation of phosphate metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
GOC:go_curators
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
GO:0044246
regulation of metabolism
regulation of multicellular organismal metabolic process
regulation of organismal metabolic process
biological_process
GO:0019222
regulation of metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
GOC:go_curators
regulation of organismal metabolic process
GOC:tb
The attachment of a cell or organism to a substrate, another cell, or other organism. Biological adhesion includes intracellular attachment between membrane regions.
biological_process
GO:0022610
biological adhesion
The attachment of a cell or organism to a substrate, another cell, or other organism. Biological adhesion includes intracellular attachment between membrane regions.
GOC:isa_complete
Any process that modulates the frequency, rate or extent of a signaling process.
2010-02-16T09:30:50Z
biological_process
regulation of signaling process
regulation of signalling process
GO:0023051
regulation of signaling
Any process that modulates the frequency, rate or extent of a signaling process.
GOC:mtg_signal
regulation of signaling process
GOC:bf
regulation of signalling process
GOC:mah
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.
janelomax
2010-02-16T09:30:50Z
GO:0023046
GO:0044700
biological signaling
signaling process
signalling
biological_process
signalling process
single organism signaling
GO:0023052
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.
signaling
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.
GOC:mtg_signal
GOC:mtg_signaling_feb11
GOC:signaling
signalling process
GOC:mah
Any process that activates, maintains or increases the frequency, rate or extent of a signaling process.
2010-02-16T09:30:50Z
positive regulation of signalling process
biological_process
positive regulation of signaling process
GO:0023056
positive regulation of signaling
Any process that activates, maintains or increases the frequency, rate or extent of a signaling process.
GOC:mtg_signal
positive regulation of signalling process
GOC:mah
positive regulation of signaling process
GOC:bf
Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process.
2010-02-16T09:30:50Z
biological_process
negative regulation of signaling process
negative regulation of signalling process
GO:0023057
negative regulation of signaling
Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process.
GOC:mtg_signal
negative regulation of signaling process
GOC:bf
negative regulation of signalling process
GOC:mah
The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is changed.
MIPS_funcat:18.02.07
molecular_function
GO:0030545
receptor regulator activity
The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is changed.
GOC:ceb
The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased.
receptor activator activity
molecular_function
GO:0030546
signaling receptor activator activity
The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased.
GOC:ceb
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 metabolism
biological_process
GO:0031323
regulation of cellular metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
GOC:mah
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
biological_process
GO:0031324
negative 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.
GOC:mah
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
biological_process
GO:0031325
positive 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.
GOC:mah
Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
down regulation of protein binding
down-regulation of protein binding
downregulation of protein binding
inhibition of protein binding
biological_process
GO:0032091
negative regulation of protein binding
Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
GOC:mah
Any process that activates or increases the frequency, rate or extent of protein binding.
up regulation of protein binding
up-regulation of protein binding
upregulation of protein binding
activation of protein binding
stimulation of protein binding
biological_process
GO:0032092
positive regulation of protein binding
Any process that activates or increases the frequency, rate or extent of protein binding.
GOC:mah
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.
regulation of localisation
biological_process
GO:0032879
regulation of localization
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.
GOC:mah
regulation of localisation
GOC:mah
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.
down regulation of kinase activity
down-regulation of kinase activity
downregulation of kinase activity
inhibition of kinase activity
kinase inhibitor
biological_process
GO:0033673
negative regulation of kinase activity
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.
GOC:mah
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.
up regulation of kinase activity
up-regulation of kinase activity
upregulation of kinase activity
kinase activator
stimulation of kinase activity
biological_process
GO:0033674
positive regulation of kinase activity
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.
GOC:mah
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.
rfoulger
2011-08-01T02:45:27Z
GO:0004872
GO:0019041
receptor activity
receptor activity involved in signal transduction
molecular_function
GO:0038023
signaling receptor activity
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.
GOC:bf
GOC:signaling
receptor activity involved in signal transduction
GOC:bf
Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule.
biological_process
GO:0042325
regulation of phosphorylation
Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule.
GOC:jl
Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule.
down regulation of phosphorylation
down-regulation of phosphorylation
downregulation of phosphorylation
inhibition of phosphorylation
biological_process
GO:0042326
negative regulation of phosphorylation
Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule.
GOC:jl
Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule.
up regulation of phosphorylation
up-regulation of phosphorylation
upregulation of phosphorylation
activation of phosphorylation
stimulation of phosphorylation
biological_process
GO:0042327
positive regulation of phosphorylation
Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule.
GOC:jl
Any process that activates or increases the activity of an enzyme.
GO:0048554
MIPS_funcat:18.02.01.01
positive regulation of enzyme activity
up regulation of enzyme activity
up-regulation of enzyme activity
upregulation of enzyme activity
activation of enzyme activity
activation of metalloenzyme activity
positive regulation of metalloenzyme activity
stimulation of enzyme activity
stimulation of metalloenzyme activity
up regulation of metalloenzyme activity
up-regulation of metalloenzyme activity
upregulation of metalloenzyme activity
biological_process
GO:0043085
positive regulation of catalytic activity
Any process that activates or increases the activity of an enzyme.
GOC:ebc
GOC:jl
GOC:tb
GOC:vw
positive regulation of enzyme activity
GOC:tb
Any process that stops or reduces the activity of an enzyme.
GO:0048553
down regulation of enzyme activity
down-regulation of enzyme activity
down-regulation of metalloenzyme activity
downregulation of enzyme activity
negative regulation of enzyme activity
down regulation of metalloenzyme activity
downregulation of metalloenzyme activity
inhibition of enzyme activity
inhibition of metalloenzyme activity
negative regulation of metalloenzyme activity
biological_process
GO:0043086
negative regulation of catalytic activity
Any process that stops or reduces the activity of an enzyme.
GOC:ebc
GOC:jl
GOC:tb
GOC:vw
negative regulation of enzyme activity
GOC:tb
Any process that modulates the frequency, rate or extent of protein binding.
biological_process
GO:0043393
regulation of protein binding
Any process that modulates the frequency, rate or extent of protein binding.
GOC:go_curators
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.
biological_process
GO:0043549
regulation of kinase activity
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.
GOC:bf
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.
biological_process
GO:0043900
regulation of multi-organism process
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.
GOC:jl
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.
biological_process
GO:0043901
negative regulation of multi-organism process
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.
GOC:jl
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.
biological_process
GO:0043902
positive 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.
GOC:jl
Any process that modulates the frequency, rate or extent of symbiosis, an interaction between two organisms living together in more or less intimate association.
biological_process
GO:0043903
regulation of symbiosis, encompassing mutualism through parasitism
Any process that modulates the frequency, rate or extent of symbiosis, an interaction between two organisms living together in more or less intimate association.
GOC:jl
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.
jane
2009-04-21T04:07:27Z
biological_process
GO:0044092
negative regulation of molecular function
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.
GO:jl
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.
jane
2009-04-21T04:11:06Z
biological_process
GO:0044093
positive 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.
GO:jl
The chemical reactions and pathways by which individual cells transform chemical substances.
cellular metabolism
biological_process
intermediary metabolism
GO:0044237
cellular metabolic process
The chemical reactions and pathways by which individual cells transform chemical substances.
GOC:go_curators
intermediary metabolism
GOC:mah
true
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.
GO:0043298
GO:0044404
GO:0072519
GO:0085031
commensalism
host-pathogen interaction
parasitism
biological_process
symbiosis
symbiosis, encompassing mutualism through parasitism
symbiotic interaction
symbiotic interaction between host and organism
symbiotic interaction between organisms
symbiotic interaction between species
GO:0044403
Changed term, definition see https://github.com/geneontology/go-ontology/issues/14807
symbiosis, encompassing mutualism through parasitism
symbiotic process
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.
GOC:cc
https://study.com/academy/lesson/symbiont-definition-lesson-quiz.html
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.
GO:0051825
GO:0051856
adhesion to other organism involved in symbiotic interaction
adhesion to host
adhesion to symbiont
host adhesion
biological_process
adhesion to other organism during symbiotic interaction
GO:0044406
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.
adhesion of symbiont to host
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.
GOC:bf
GOC:cc
GOC:dos
GOC:jl
adhesion to other organism during symbiotic interaction
GOC:dph
Any process in which an organism has an effect on an organism of a different species.
interaction with another species
interspecies interaction
interspecies interaction with other organisms
biological_process
GO:0044419
interspecies interaction between organisms
Any process in which an organism has an effect on an organism of a different species.
GOC:cc
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
biological_process
GO:0045936
negative regulation of phosphate metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
GOC:go_curators
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
biological_process
GO:0045937
positive regulation of phosphate metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
GOC:go_curators
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).
midori
2010-09-13T04:51:59Z
GO:0071884
receptor agonist activity
signaling molecule
signaling receptor ligand activity
vitamin D receptor activator activity
molecular_function
GO:0048018
Definition discussed in https://github.com/geneontology/go-ontology/issues/14220
receptor ligand activity
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).
GOC:kv
GOC:molecular_function_refactoring
GOC:pdt
receptor agonist activity
GOC:molecular_function_refactoring
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.
GO:0043119
positive regulation of physiological process
up regulation of biological process
up-regulation of biological process
upregulation of biological process
activation of biological process
stimulation of biological process
biological_process
GO:0048518
positive regulation of biological process
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.
GOC:jid
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.
GO:0043118
down regulation of biological process
down-regulation of biological process
downregulation of biological process
negative regulation of physiological process
inhibition of biological process
biological_process
GO:0048519
negative 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.
GOC:jid
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.
GO:0051242
positive regulation of cellular physiological process
up regulation of cellular process
up-regulation of cellular process
upregulation of cellular process
activation of cellular process
stimulation of cellular process
biological_process
GO:0048522
positive regulation of cellular 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.
GOC:jid
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.
GO:0051243
down regulation of cellular process
down-regulation of cellular process
downregulation of cellular process
negative regulation of cellular physiological process
inhibition of cellular process
biological_process
GO:0048523
negative regulation of cellular 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.
GOC:jid
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.
biological_process
GO:0048583
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.
regulation of response to stimulus
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.
GOC:jid
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.
up regulation of response to stimulus
up-regulation of response to stimulus
upregulation of response to stimulus
activation of response to stimulus
stimulation of response to stimulus
biological_process
GO:0048584
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.
positive regulation of response to stimulus
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.
GOC:jid
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.
down regulation of response to stimulus
down-regulation of response to stimulus
downregulation of response to stimulus
inhibition of response to stimulus
biological_process
GO:0048585
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.
negative 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.
GOC:jid
Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
biological_process
GO:0050776
regulation of immune response
Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
GOC:ai
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.
down regulation of immune response
down-regulation of immune response
downregulation of immune response
inhibition of immune response
biological_process
GO:0050777
negative regulation of immune response
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.
GOC:ai
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.
up regulation of immune response
up-regulation of immune response
upregulation of immune response
stimulation of immune response
biological_process
GO:0050778
positive regulation of immune response
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.
GOC:ai
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.
GO:0050791
regulation of physiological process
biological_process
GO:0050789
regulation of biological process
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.
GOC:ai
GOC:go_curators
Any process that modulates the activity of an enzyme.
GO:0048552
MIPS_funcat:18.02.01
regulation of enzyme activity
regulation of metalloenzyme activity
biological_process
GO:0050790
regulation of catalytic activity
Any process that modulates the activity of an enzyme.
GOC:ai
GOC:ebc
GOC:vw
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.
GO:0051244
regulation of cellular physiological process
biological_process
GO:0050794
regulation of cellular process
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.
GOC:go_curators
response to stimulus
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.
GO:0051869
MIPS_funcat:34.11
physiological response to stimulus
biological_process
GO:0050896
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.
response to stimulus
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.
GOC:ai
GOC:bf
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.
biological_process
GO:0051098
regulation of binding
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.
GOC:ai
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.
up regulation of binding
up-regulation of binding
upregulation of binding
activation of binding
stimulation of binding
biological_process
GO:0051099
positive regulation of binding
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.
GOC:ai
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.
down regulation of binding
down-regulation of binding
downregulation of binding
inhibition of binding
biological_process
GO:0051100
negative regulation of binding
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.
GOC:ai
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
regulation of phosphorus metabolism
biological_process
GO:0051174
regulation of phosphorus metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
GOC:ai
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.
jl
2013-12-18T13:51:04Z
GO:1902578
establishment and maintenance of localization
establishment and maintenance of position
localisation
establishment and maintenance of cellular component location
establishment and maintenance of substance location
establishment and maintenance of substrate location
biological_process
single organism localization
single-organism localization
GO:0051179
localization
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.
GOC:ai
GOC:dos
localisation
GOC:mah
single organism localization
GOC:TermGenie
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
establishment of localisation
biological_process
GO:0051234
establishment of localization
Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.
GOC:ai
GOC:dos
establishment of localisation
GOC:mah
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.
transferase regulator
biological_process
GO:0051338
This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.
regulation of transferase activity
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.
EC:2.-.-.-
GOC:ai
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.
transferase activator
up regulation of transferase activity
up-regulation of transferase activity
upregulation of transferase activity
activation of transferase activity
stimulation of transferase activity
biological_process
GO:0051347
This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.
positive regulation of transferase activity
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.
GOC:ai
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.
down regulation of transferase activity
down-regulation of transferase activity
downregulation of transferase activity
transferase inhibitor
inhibition of transferase activity
biological_process
GO:0051348
This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.
negative 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.
GOC:ai
A biological process which involves another organism of the same or different species.
GO:0051706
interaction between organisms
physiological interaction between organisms
physiological interaction with other organism
biological_process
GO:0051704
multi-organism process
A biological process which involves another organism of the same or different species.
GOC:jl
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.
biological_process
GO:0051716
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.
cellular response to stimulus
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.
GOC:bf
GOC:jl
A compound molecular function in which an effector function is controlled by one or more regulatory components.
molecular_function
GO:0060089
molecular transducer activity
A compound molecular function in which an effector function is controlled by one or more regulatory components.
GOC:dos
GOC:pdt
Any process that modulates a measurable attribute of any biological process, quality or function.
regulation
biological_process
GO:0065007
biological regulation
Any process that modulates a measurable attribute of any biological process, quality or function.
GOC:dph
GOC:isa_complete
GOC:mah
GOC:pr
GOC:vw
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.
regulation of a molecular function
biological_process
GO:0065009
regulation of molecular 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.
GOC:isa_complete
A molecular function that modulates the activity of a gene product or complex. Examples include enzyme regulators and channel regulators.
molecular_function
GO:0098772
molecular function regulator
A molecular function that modulates the activity of a gene product or complex. Examples include enzyme regulators and channel regulators.
GOC:dos
GOC:pt
Any process that modulates the frequency, rate or extent of a protein or other molecule binding to a receptor.
bf
2012-02-22T11:40:53Z
regulation of receptor ligand
biological_process
GO:1900120
regulation of receptor binding
Any process that modulates the frequency, rate or extent of a protein or other molecule binding to a receptor.
GOC:TermGenie
GOC:signaling
regulation of receptor ligand
GOC:TermGenie
Any process that stops, prevents or reduces the frequency, rate or extent of a protein or other molecule binding to a receptor.
bf
2012-02-22T11:40:57Z
down regulation of receptor binding
down-regulation of receptor binding
downregulation of receptor binding
inhibition of receptor binding
inhibition of receptor ligand
biological_process
down regulation of receptor-associated protein activity
GO:1900121
negative regulation of receptor binding
Any process that stops, prevents or reduces the frequency, rate or extent of a protein or other molecule binding to a receptor.
GOC:TermGenie
GOC:signaling
down regulation of receptor binding
GOC:TermGenie
down-regulation of receptor binding
GOC:TermGenie
downregulation of receptor binding
GOC:TermGenie
inhibition of receptor binding
GOC:TermGenie
inhibition of receptor ligand
GOC:TermGenie
down regulation of receptor-associated protein activity
GOC:TermGenie
Any process that activates or increases the frequency, rate or extent of a protein or other molecule binding to a receptor.
bf
2012-02-22T11:41:00Z
up regulation of receptor binding
upregulation of receptor binding
activation of receptor binding
biological_process
GO:1900122
positive regulation of receptor binding
Any process that activates or increases the frequency, rate or extent of a protein or other molecule binding to a receptor.
GOC:TermGenie
GOC:signaling
up regulation of receptor binding
GOC:TermGenie
upregulation of receptor binding
GOC:TermGenie
activation of receptor binding
GOC:TermGenie
Any process that stops, prevents or reduces the frequency, rate or extent of a signaling receptor activity.
rfoulger
2010-12-02T09:28:47Z
negative regulation of receptor activity
biological_process
GO:2000272
negative regulation of signaling receptor activity
Any process that stops, prevents or reduces the frequency, rate or extent of a signaling receptor activity.
GOC:obol
Any process that activates or increases the frequency, rate or extent of signaling receptor activity.
rfoulger
2010-12-02T09:28:50Z
biological_process
GO:2000273
positive regulation of signaling receptor activity
Any process that activates or increases the frequency, rate or extent of signaling receptor activity.
GOC:obol
measurement unit label
Examples of measurement unit labels are liters, inches, weight per volume.
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
2009-03-16: provenance: a term measurement unit was
proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and
Cristian Cocos, and subsequently moved to IAO where the objective for
which the original term was defined was satisfied with the definition
of this, different, term.
2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
measurement unit label
objective specification
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
Answers the question, why did you do this experiment?
PERSON: Alan Ruttenberg
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
OBI_0000217
objective specification
Pour the contents of flask 1 into flask 2
a directive information entity that describes an action the bearer will take
Alan Ruttenberg
OBI Plan and Planned Process branch
action specification
datum label
A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n
GROUP: IAO
9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
datum label
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: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Chris Stoeckert
PERSON: Melanie Courtot
GROUP: OBI
software
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.
PERSON: Alan Ruttenberg
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
information carrier
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
JAR: datum -- well, this will be very tricky to define, but maybe some
information-like stuff that might be put into a computer and that is
meant, by someone, to denote and/or to be interpreted by some
process... I would include lists, tables, sentences... I think I might
defer to Barry, or to Brian Cantwell Smith
JAR: A data item is an approximately justified approximately true approximate belief
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
data item
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
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.
PERSON: Chris Stoeckert
OBI_0000142
information content 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
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
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
OBI_0000123
group:OBI
dot plot
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
person:Alan Ruttenberg
person:Allyson Lister
OBI_0000240
group:OBI
graph
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
OBI_0000270
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
algorithm
curation status specification
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
PERSON:Bill Bug
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
OBI_0000266
curation status specification
data 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"
PERSON: Alan Ruttenberg
PlanAndPlannedProcess Branch
OBI branch derived
OBI_0000187
data format specification
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.
person:Allyson Lister
person:Chris Stoeckert
OBI_0000042
group:OBI
data set
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.
person:Alan Ruttenberg
person:Allyson
person:Chris Stoeckert
OBI_0000030
group:OBI
image
data about an ontology part is a data item about a part of an ontology, for example a term
Person:Alan Ruttenberg
data about an ontology part
plan specification
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2014-03-31: A plan specification can have other parts, such as conditional specifications.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
Alan Ruttenberg
OBI Plan and Planned Process branch
OBI_0000344
2/3/2009 Comment from OBI review.
Action specification not well enough specified.
Conditional specification not well enough specified.
Question whether all plan specifications have objective specifications.
Request that IAO either clarify these or change definitions not to use them
plan specification
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.
GROUP: IAO
material information bearer
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
PERSON:Melanie Courtot
GROUP:OBI
histogram
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.
PERSON:Chris Stoeckert
PERSON:James Malone
PERSON:Melanie Courtot
GROUP:OBI
heatmap
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.
PERSON:Chris Stoeckert
PERSON:James Malone
PERSON:Melanie Courtot
WEB: http://en.wikipedia.org/wiki/Dendrogram
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.
PERSON:Chris Stoeckert
PERSON:James Malone
PERSON:Melanie Courtot
scattergraph
WEB: http://en.wikipedia.org/wiki/Scatterplot
scatter plot
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.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
obsolescence reason specification
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.
PERSON: Lawrence Hunter
figure
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
PERSON: Lawrence Hunter
diagram
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
PERSON: Lawrence Hunter
document
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.
Alan Ruttenberg
Barry Smith, Werner Ceusters
denotator type
A role borne by an infectious agent when contained in a host in which its infectious disposition can be realized.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
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.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
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.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
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.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
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.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
The role is realized in a process by which the infectious disorder is established in the host.
secondary infection role
A disease whose physical basis is an infectious disorder.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
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.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
The disposition is realized in an adherence to host process.
adhesion disposition
A disposition to initiate processes that result in a disorder.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
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.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
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.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
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.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
susceptibility to infectious agent
An infection comprised of infectious organisms from different Species.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
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.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
extracellular infection
An infection for which the infectious agents that are part of the infection persist inside host cells.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
intracellular infection
An infection for which the infectious agents that are part of the infection are distributed throughout the host.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
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.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
local infection
A local infection for which symptoms are observed in parts of the host's extended organism that are distant from the infection.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
focal infection
An infectious disease course that begins soon after infection is established and progresses rapidly to severe stages.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
acute infectious disease course
A disease course that is the realization of an infectious disease.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
infectious disease course
An infection that is clinically abnormal.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
infectious disorder
An infection that has as part virus particles located in the blood.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
viremia
An infection that has as part bacteria located in the blood.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
bacteremia
A material entity with a pathogenic disposition.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
pathogen
An organism bearing a host role.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
host
A biological macromolecule produced by a pathogen and that has a virulence factor disposition.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
virulence factor
A biological macromolecule that has an adhesion disposition.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
adhesin
adhesion molecule
adhesion factor
An infection bearing the primary infection role.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
primary infection
An infection bearing the secondary infection role.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
secondary infection
An infection that is part of an asymptomatic host.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
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.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
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.
infection
An organism that has an infectious disposition.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
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.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
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.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
appearance of disorder
An infectious disorder that is the physical basis for an unfolding acute infectious disease course.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
acute infection
An infection that persists for an extended period of time.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
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.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
host role
An infection resulting from a transmission process that unfolds in a hospital.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
nosocomial infection
hospital-acquired infection
An infection resulting from a transmission process that did not unfold in a health care facility.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
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.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
metatstatic infection
An infection resulting from a transmission process that unfolds in a nursing home.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
nursing-home acquired infection
An infection comprised of infectious organisms all of the same Species.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
simple infection
An infection that has as part organisms of the Genus Candida.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
candidiasis
An infection that has as part organisms of the Species Trichomonas vaginalis.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
trichomoniasis
An infection that has as part organisms of the Genus Leptospira.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
leptospirosis
An infection located in the bowel and that has as part organisms of the Genus Shigella.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
Shigellosis
An infection located in the colon and that has as part organisms of the Species Entamoeba histolytica
Albert Goldfain
Alexander Diehl
Lindsay Cowell
amebiasis
Interaction is a processual entity that has two or more participants (i.e., interactors) that have an effect upon one another.
YH, ZX
interact, interacted, interacting, interaction, interaction, interactor, interactors, interacts, participates; plays a role, contribute, contributed, contributes, contributing, engagement, engagements, engages, engaging, involve, involved, involves, involving, act, acted, acting, acts
interaction
an regulator role that is borne by a material entity that regulates an interaction.
YH
regulator role
an interactor role that is borne by a material entity that acts as an input of an interaction.
YH, ZX
interaction input role
input interactor role
an interactor role that is borne by a material entity that acts as an output of an interaction.
YH, ZX
interaction output role
output interactor role
a positive regulator role that is borne by a material entity that activates an interaction.
YH
activator role
a role that is borne by a material entity to act as a participant in an interaction process.
YH, ZX
interactor role
an interactor role that is played by a material entity that starts or speeds up a chemical reaction while undergoing no permanent change itself.
YH
chemical reaction catalyst role
an interactor role that is borne by a material entity that positively regulates an interaction.
YH
positive regulator role
an interactor role that is borne by a material entity that negatively regulates an interaction.
YH
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).
YH
deactivator role
an input interactor role that is borne by a material entity that motivates a process.
Oliver He
https://en.wikipedia.org/wiki/Motivation#Herzberg's_two-factor_theory
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.
Oliver He
https://en.wikipedia.org/wiki/Motivation#Herzberg's_two-factor_theory
hygiene factor role
GC_ID:1
hamsters
ncbi_taxonomy
Cricetinae
ncbi_taxonomy
Cgri-
Chinese hamster
NCBITaxon:10029
Cricetulus griseus
Cricetulus griseus
灰仓鼠
Cgri-
PRO:DAN
Chinese hamster
golden hamster
ncbi_taxonomy
NCBITaxon:10036
Mesocricetus auratus
golden hamster
GC_ID:1
gerbils
ncbi_taxonomy
Gerbillinae
GC_ID:1
Mongolian gerbil
Mongolian jird
ncbi_taxonomy
Meriones unguiculatus
GC_ID:1
PMID:15371245
ncbi_taxonomy
Muridae
GC_ID:1
Mus
mice
mouse
ncbi_taxonomy
Mus <mouse, genus>
Mus musculus
house mouse
mouse
NCBITaxon:85055
GC_ID:1
house mouse
mouse
ncbi_taxonomy
Mus muscaris
m
mice C57BL/6xCBA/CaJ hybrid
mouse
NCBITaxon:10090
Mus musculus
Mus musculus
小家鼠
m
PRO:DAN
mouse
GC_ID:1
rat
rats
ncbi_taxonomy
Rattus
GC_ID:1
chinchillas
chinchillas and viscachas
ncbi_taxonomy
Chinchillidae
Viruses
GC_ID:1
Viruses
ncbi_taxonomy
Vira
Viridae
viral-
viruses
NCBITaxon:10239
Viruses
virus
viral-
PRO:DAN
GC_ID:1
ncbi_taxonomy
Chordopoxvirinae
GC_ID:1
ncbi_taxonomy
Orthopoxvirus
CPXV
GC_ID:1
ncbi_taxonomy
cowpox virus CPV
Cowpox virus
GC_ID:1
ncbi_taxonomy
vaccinia virus VV
Vaccinia virus
GC_ID:1
ncbi_taxonomy
Vaccinia virus (strain Tian Tan)
Vaccinia virus Tian Tan
GC_ID:1
ncbi_taxonomy
Vaccinia virus (strain WR)
NCBITaxon:10254
Vaccinia virus WR
GC_ID:1
ncbi_taxonomy
Contagious pustular dermatitis virus
orf virus OV
Orf virus
SPPV
GC_ID:1
ncbi_taxonomy
sheep pox virus
Sheeppox virus
GC_ID:1
ncbi_taxonomy
Leporipoxvirus
SFV
GC_ID:1
ncbi_taxonomy
Shope fibroma virus
Shope fibroma virus SFV
Rabbit fibroma virus
GC_ID:1
ncbi_taxonomy
myxoma virus MYX
Myxoma virus
GC_ID:1
ncbi_taxonomy
H5N1
H5N1 subtype
Herpesviridae
GC_ID:1
ncbi_taxonomy
Herpesviridae
GC_ID:1
ncbi_taxonomy
Alphaherpesvirinae
GC_ID:1
ncbi_taxonomy
Simplexvirus
HSV-1
HSV1
GC_ID:1
Herpes simplex virus type 1
ncbi_taxonomy
Herpes simplex virus 1
Human Herpesvirus-1
Human herpesvirus 1
Human herpesvirus type 1
herpes simplex virus 1 HSV-1
herpes simplex virus HSV-1
herpes simplex virus type 1 HSV-1
herpes simplex virus type 1 HSV1
herpes simplex virus type-1 HSV-1
NCBITaxon:10298
Human alphaherpesvirus 1
Human herpesvirus 1
HSV1
GC_ID:1
HSV1(17)
ncbi_taxonomy
NCBITaxon:10299
Herpes simplex virus (type 1 / strain 17)
Herpes simplex virus type 1 strain 17
HSV1(17)
PRO:DAN
HSV2
GC_ID:1
ncbi_taxonomy
Herpes simplex virus (type 2)
Herpes simplex virus 2
Herpes simplex virus type 2
herpes simplex virus type 2 HSV-2
Human herpesvirus 2
GC_ID:1
ncbi_taxonomy
Varicellovirus
NCBITaxon:11265
NCBITaxon:12738
BoHV-1
GC_ID:1
ncbi_taxonomy
Bovine herpesvirus 1
Bovine herpesvirus type 1
Bovine herpesvirus-1
Bovine rhinotracheitis virus
Infectious bovine rhinotracheitis virus
bovine herpesvirus 1 BHV 1
bovine herpesvirus 1 BHV-1
bovine herpesvirus 1 BHV1
bovine herpesvirus BHV-1
bovine herpesvirus type 1 BHV-1
bovine herpesvirus type-1 BHV-1
infectious bovine rhinotracheitis virus BHV-1
Bovine alphaherpesvirus 1
Bovine herpesvirus 1
EHV-1
GC_ID:1
Equine herpesvirus 1
ncbi_taxonomy
Equid herpesvirus 1
Equine herpesvirus type 1
Equine herpesvirus-1
equine abortion virus
equine herpesvirus 1 EHV-1
equine herpesvirus type 1 EHV-1
equine herpesvirus type 1 EVH-1
equine herpesvirus type-1
Equid alphaherpesvirus 1
Equid herpesvirus 1
GC_ID:1
ncbi_taxonomy
Felid herpesvirus 1
Feline herpesvirus 1
Feline herpesvirus type 1
Feline viral rhinotracheitis virus
feline herpesvirus
feline herpesvirus type 1 FHV-1
feline herpesvirus-1
feline herpesvirus-1 FHV-1
NCBITaxon:10334
Felid alphaherpesvirus 1
Felid herpesvirus 1
HHV-3
VZV
GC_ID:1
Varicella-zoster virus
ncbi_taxonomy
Human alphaherpesvirus 3
Varicella Zoster Virus
varicella zoster virus VZV
varicella-zoster virus VZV
Human herpesvirus 3
NCBITaxon:44156
PRV
GC_ID:1
Pseudorabies virus
ncbi_taxonomy
Alphaherpesvirus pseudorabies virus PRV
Aujeszky's disease virus
Pseudorabies Virus PRV
Pseudorabies virus
Suid herpesvirus 1
Suid herpesvirus type 1
Suid alphaherpesvirus 1
Suid herpesvirus 1
NCBITaxon:10342
NCBITaxon:12743
NCBITaxon:46620
GaHV-1
ILTV
GC_ID:1
ncbi_taxonomy
Avian infectious laryngotracheitis virus
Gallid herpesvirus 1
Gallid herpesvirus type 1
Infectious laryngotracheitis virus
Laryngotracheitis virus
infectious laryngotracheitis virus ILTV
Gallid alphaherpesvirus 1
Gallid herpesvirus 1
NCBITaxon:38013
NCBITaxon:39111
NCBITaxon:43684
GaHV-2
MDV1
GC_ID:1
Marek disease virus type 1
ncbi_taxonomy
Gallid herpesvirus 1 (serotype 1)
Gallid herpesvirus type 2
Marek disease virus
Marek's disease herpesvirus
Marek's disease herpesvirus 1
Marek's disease virus
Marek's disease virus (MDV)
Marek's disease virus MDV
Marek's disease virus MDV1
Marek's disease virus serotype 1 MDV-1
Marek's disease virus type 1
Marek's disease virus type 1 MDV1
Gallid herpesvirus 2
GC_ID:1
ncbi_taxonomy
Obtectomera
ASFV
GC_ID:1
ncbi_taxonomy
African swine fever virus ASF
African swine fever virus ASFV
African swine fever virus, ASFV
African swine fever virus
PPV
GC_ID:1
ncbi_taxonomy
porcine parvovirus PPV
Porcine parvovirus
GC_ID:1
ncbi_taxonomy
Rotaviruses
Rotavirus
GC_ID:1
arboviruses group A
ncbi_taxonomy
Alphaviridae
Alphavirus
RRV
GC_ID:1
ncbi_taxonomy
Ross River virus
GC_ID:1
ncbi_taxonomy
Sindbis virus dsSIN
Sindbis virus
VEE
VEEV
GC_ID:1
ncbi_taxonomy
Venezuelan equine encephalitis VEE
Venezuelan equine encephalitis virus VEE
Venezuelan equine encephalomyelitis virus
Venezuelan equine encephalitis virus
GC_ID:1
ncbi_taxonomy
Western equine encephaliomyelitis virus
Western equine encephalitis virus
Western equine encephalomyelitis virus
Western equine encephalitis virus
Western equine encephalomyelitis virus
GC_ID:1
ncbi_taxonomy
Flavivirus (arbovirus group B)
Flaviviridae
GC_ID:1
arboviruses group B
ncbi_taxonomy
Flavivirus
WNV
GC_ID:1
ncbi_taxonomy
WNV-
NCBITaxon:11082
West Nile virus
WNV-
PRO:DAN
TBEV
GC_ID:1
ncbi_taxonomy
FSME virus
tick-borne encephalitis virus TBE virus
tick-borne encephalitis virus TBEV
Tick-borne encephalitis virus
YFV
GC_ID:1
ncbi_taxonomy
Flavivirus febricis
yellow fever virus YFV
Yellow fever virus
NCBITaxon:12625
NCBITaxon:54314
GC_ID:1
PMID:7747470
ncbi_taxonomy
Hog cholera virus
Pestivirus type 2
classical swine fever virus CSFV
hog cholera virus HCV
swine fever virus
Classical swine fever virus
GC_ID:1
ncbi_taxonomy
Hog cholera virus (strain Brescia)
Hog cholera virus - Brescia
Classical swine fever virus - Brescia
FIPV
GC_ID:1
FIPV
ncbi_taxonomy
Feline infectious peritonitis virus
GC_ID:1
ncbi_taxonomy
porcine respiratory coronavirus PRCV
porcine respiratory virus
Porcine respiratory coronavirus
GC_ID:11
PMID:11155970
ncbi_taxonomy
Bartonella birtlesii
GC_ID:11
ncbi_taxonomy
pseudomallei group
GC_ID:1
negative-sense genome single-stranded RNA viruses
ncbi_taxonomy
Mononegavirales
GC_ID:1
ncbi_taxonomy
Paramyxoviridae
GC_ID:1
ncbi_taxonomy
Paramyxovirinae
NDV
GC_ID:1
ncbi_taxonomy
Avian paramyxovirus type 1
Newcastle disease virus NDV
avian paramyxovirus 1
Newcastle disease virus
NCBITaxon:11202
GC_ID:1
ncbi_taxonomy
Human parainfluenza 3 virus
Human parainfluenza virus type 3
Parainfluenza virus type 3
human parainfluenza virus 3 HPIV3
human parainfluenza virus type 3 PIV3
parainfluenza virus type 3 PIV-3
Human parainfluenza virus 3
NCBITaxon:11230
GC_ID:1
ncbi_taxonomy
Cell-associated subacute sclerosing panencephalitis
Measles virus
Subacute sclerosing panencephalitis virus
measles virus MV
rougeole virus
rubeola virus
subacute sclerose panencephalitis virus
subacute sclerosing panencephalitis virus, SSPEV
Measles morbillivirus
Measles virus
GC_ID:1
ncbi_taxonomy
Pneumovirinae
Pneumoviridae
Pneumovirinae
GC_ID:1
ncbi_taxonomy
Pneumovirus
NCBITaxon:12604
BRS
BRSV
GC_ID:1
ncbi_taxonomy
Bovine respiratory syncytial virus
bovine RSV
bovine respiratory syncytial virus BRSV
Bovine orthopneumovirus
Bovine respiratory syncytial virus
HRSV
GC_ID:1
ncbi_taxonomy
Human respiratory syncytial virus
human RSV
Human orthopneumovirus
GC_ID:1
ncbi_taxonomy
Human respiratory syncytial virus (strain A2)
Human respiratory syncytial virus A2
GC_ID:1
PMID:16186241
ncbi_taxonomy
Rhabdoviridae
IHNV
GC_ID:1
ncbi_taxonomy
Infectious haematopoietic necrosis virus
Infectious hematopoietic necrosis virus
GC_ID:1
ncbi_taxonomy
Rabies virus
Rabies lyssavirus
Rabies virus
GC_ID:1
ncbi_taxonomy
Influenza virus
Influenza virus sp.
Influenzavirus
avian influenza virus
unidentified influenza virus
FLUAV
GC_ID:1
ncbi_taxonomy
Influenza virus type A
influenza A virus INF A
NCBITaxon:11320
Influenza A virus
GC_ID:1
ncbi_taxonomy
Bunyaviridae
GC_ID:11
PMID:10192388
PMID:10871362
ncbi_taxonomy
Chlamydia pneumoniae CWL029
Chlamydophila pneumoniae CWL029
GC_ID:1
ncbi_taxonomy
Bunyavirus la crosse
La Crosse virus
RVFV
GC_ID:1
ncbi_taxonomy
Rift Valley fever virus
GC_ID:1
ncbi_taxonomy
Korean hemorrhagic fever virus
Hantaan virus
GC_ID:1
ncbi_taxonomy
Lentivirinae
Lentivirus
Primate lentivirus group
GC_ID:1
ncbi_taxonomy
Primate immunodeficiency viruses
Primate lentivirus group
FIV
GC_ID:1
ncbi_taxonomy
feline immunodeficiency virus FIV
Feline immunodeficiency virus
Human immunodeficiency virus 1
HIV
HIV-1
HIV1
LAV-1
GC_ID:1
ncbi_taxonomy
AIDS virus
Human immundeficiency virus type 1
Human immunodeficiencey virus type 1
Human immunodeficiency virus type 1
human immunodeficiency virus 1 HIV-1
human immunodeficiency virus HIV-1
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
human immunodeficiency virus-1 HIV-1
Human immunodeficiency virus 1
NCBITaxon:11677
NCBITaxon:11739
NCBITaxon:11740
CIV
SIV
GC_ID:1
ncbi_taxonomy
Chimpanzee immunodeficiency virus
Chimpanzee immunodeficiency virus (SIV(CPZ))
Simian immunodeficiency virus SIVcpz
simian immunodeficiency virus SIV
simian immunodeficiency virus, SIV
simian immunodeficiency viruses SIV
Simian immunodeficiency virus
GC_ID:1
fish
fishes
ncbi_taxonomy
Agnatha
Hyperotreti
Euteleostomi
bony vertebrates
NCBITaxon:40673
GC_ID:1
bony vertebrates
ncbi_taxonomy
Euteleostomi
ncbi_taxonomy
NCBITaxon:118882
Brucellaceae
GC_ID:11
PMID:16280474
ncbi_taxonomy
Legionellaceae group
Legionellales Garrity et al. 2005
Legionellales
GC_ID:11
PMID:5462048
ncbi_taxonomy
Francisella tularensis var. palaearctica
Francisella tularensis subsp. holarctica
Ecdysozoa
GC_ID:1
ncbi_taxonomy
Ecdysozoa
EMCV
GC_ID:1
ncbi_taxonomy
encephalomyocarditis virus EMCV
encephalomyocarditis virus, EMCV
Encephalomyocarditis virus
GC_ID:1
ncbi_taxonomy
NCBITaxon:121791
Nipah henipavirus
Nipah virus
GC_ID:11
PMID:11321122
PMID:11542017
PMID:11837318
PMID:16280474
PMID:26654112
purple bacteria
purple bacteria and relatives
purple non-sulfur bacteria
purple photosynthetic bacteria
purple photosynthetic bacteria and relatives
ncbi_taxonomy
Alphaproteobacteraeota
proteobacteria
Proteobacteria
GC_ID:11
PMID:10710307
ncbi_taxonomy
Neisseria meningitidis serogroup B strain MC58
NCBITaxon:122586
Neisseria meningitidis MC58
GC_ID:11
ncbi_taxonomy
Neisseria meningitidis serogroup A strain Z2491
Neisseria meningitidis Z2491
GC_ID:11
PMID:16280474
PMID:23334881
ncbi_taxonomy
Gammaproteobacteria Garrity et al. 2005
Proteobacteria gamma subdivision
Purple bacteria, gamma subdivision
g-proteobacteria
gamma proteobacteria
gamma subdivision
gamma subgroup
Gammaproteobacteria
NCBITaxon:31968
GC_ID:11
PMID:10555317
PMID:11034484
PMID:11542017
PMID:15143038
PMID:25403554
PMID:26654112
Gram-positive bacteria
low G+C Gram-positive bacteria
low GC Gram+
ncbi_taxonomy
Bacillaeota
Bacillus/Clostridium group
Clostridium group firmicutes
Firmacutes
Gram positive bacteria
Low G+C firmicutes
clostridial firmicutes
firmicutes
Firmicutes
CAV
GC_ID:1
ncbi_taxonomy
Chicken anaemia virus
Chicken infectious anemia virus
chicken anaemia agent CAA
chicken anaemia agent virus CAA
chicken anemia virus CAV
chicken anemia virus, CAV
chiken anemia agent virus
Chicken anemia virus
GC_ID:1
ncbi_taxonomy
Ectromelia mousepox virus
mousepox
mousepox virus
Ectromelia virus
HIV
GC_ID:1
ncbi_taxonomy
AIDS virus
Human immunodeficiency virus
NCBITaxon:325213
GC_ID:11
PMID:8573498
ncbi_taxonomy
Micrococcus aureus
Micrococcus pyogenes
Staph-
Staphilococcus aureus
Staphlococcus pyogenes citreus
Staphylococcus pyogenes aureus
Staphylococus aureus
Streptococcus aureus
NCBITaxon:1280
Staphylococcus aureus
Staph-
PRO:DAN
GC_ID:11
PMID:10555340
PMID:14657115
PMID:1720654
PMID:19620365
PMID:19880633
PMID:7537076
PMID:8995803
ncbi_taxonomy
Streptococcus
NCBITaxon:76757
GC_ID:11
PMID:15774692
PMID:8995807
ncbi_taxonomy
Streptoccocus de la mammite
Streptococcus agalactiae contagiosae
Streptococcus difficile
Streptococcus difficilis
Streptococcus mastitidis
Streptococcus agalactiae
GC_ID:11
ncbi_taxonomy
Diplococcus pneumoniae
Micrococcus pneumoniae
Streptococcus pneumoniae
GC_ID:11
ncbi_taxonomy
Micrococcus scarlatinae
Streptococcus erysipelatos
Streptococcus hemolyticus
Streptococcus pyrogenes
Streptococcus scarlatinae
Streptococcus pyogenes
GC_ID:11
ncbi_taxonomy
Streptococcus equi
GC_ID:11
PMID:12734250
PMID:1283774
PMID:16558776
ncbi_taxonomy
Acinetobacter mallei
Actinobacillus mallei
Bacillus mallei
Loefferella mallei
Malleomyces mallei
Pfeifferella mallei
Pseudomonas mallei
Burkholderia mallei
GC_ID:11
PMID:8427810
PMID:9103648
ncbi_taxonomy
Enterococcus
NCBITaxon:1219670
GC_ID:11
ncbi_taxonomy
Enterococcus feacalis
Enterococcus proteiformis
Enterocoque
Micrococcus ovalis
Micrococcus zymogenes
Streptococcus faecalis
Streptococcus glycerinaceus
Streptococcus liquefaciens
NCBITaxon:1351
Enterococcus faecalis
GC_ID:11
ncbi_taxonomy
Streptococcus faecium
NCBITaxon:1352
Enterococcus faecium
GC_ID:11
ncbi_taxonomy
Neisseria meningitidis (serogroup C)
Neisseria meningitidis serogroup C
GC_ID:11
PMID:11075904
PMID:11542017
PMID:16558735
PMID:1917844
ncbi_taxonomy
spirochetes
Spirochaetales
GC_ID:11
ncbi_taxonomy
Bacillus/Staphylococcus group
Bacillales
GC_ID:11
PMID:10871362
ncbi_taxonomy
Chlamydia pneumoniae (strain J138)
Chlamydophila pneumoniae J138
GC_ID:11
PMID:1380285
PMID:1503971
PMID:24744012
PMID:7699027
PMID:7981102
PMID:8995796
PMID:9336916
Borrelia burgdorferi sensu stricto
Lyme disease spirochete
ncbi_taxonomy
Borrelia burdorferi
Borrelia burgdorferi
Borrelia burgdorffragment
Borrelia burgdorferi
Borreliella burgdorferi
NCBITaxon:1494525
NCBITaxon:1494531
NCBITaxon:1494577
GC_ID:11
PMID:8123566
anthrax
anthrax bacterium
ncbi_taxonomy
Bacillus cereus var. anthracis
Bacteridium anthracis
anthrax-
NCBITaxon:1392
Bacillus anthracis
anthrax-
PRO:DAN
GC_ID:1
PMID:11743200
PMID:11791233
ncbi_taxonomy
Boreotheria
Boreoeutheria
NCBITaxon:147540
GC_ID:1
ncbi_taxonomy
Loculoascomycetes
Plectomycetes
bitunicate ascomycetes
Eurotiomycetes
NCBITaxon:69207
GC_ID:11
PMID:26643615
PMID:27488356
ncbi_taxonomy
Anaerobacter
Clostridium
NCBITaxon:29368
GC_ID:11
PMID:10028279
PMID:15244052
ncbi_taxonomy
Bacillus botulinus
Bacillus putrificus
Botulobacillus botulinus
Clostridium putrificum
Ermengemillus botulinus
Pacinia putrifica
Clostridium botulinum
NCBITaxon:1440055
NCBITaxon:1581190
GC_ID:11
PMID:23834245
PMID:27370902
PMID:27902176
Clostridium difficile
[Clostridium] difficile
ncbi_taxonomy
Bacillus difficilis
Clostridium difficile
Clostridium difficle
Peptoclostridium difficile
Clostridioides difficile
[Clostridium] difficile
GC_ID:11
PMID:11043982
ncbi_taxonomy
Yersinia enterocolitica subsp. enterocolitica
NCBITaxon:1683536
GC_ID:11
PMID:1374625
PMID:184898
ncbi_taxonomy
'Clostridium plagarum'
Bacillus perfringens
Bacterium welchii
Clostridium plagarum
NCBITaxon:1502
Clostridium perfringens
GC_ID:11
Escherichia coli O157:H7 EDL933
Escherichia coli O157:H7 strain EDL933
ncbi_taxonomy
Escherichia coli 0157:H7 EDL933
Escherichia coli O157:H7 str. EDL933
GC_ID:11
PMID:11418146
ncbi_taxonomy
Staphylococcus aureus (strain Mu50 / ATCC 700699)
NCBITaxon:158878
Staphylococcus aureus subsp. aureus Mu50
GC_ID:11
PMID:11418146
ncbi_taxonomy
Staphylococcus aureus (strain N315)
NCBITaxon:158879
Staphylococcus aureus subsp. aureus N315
GC_ID:11
PMID:11296296
Streptococcus pyogenes (serotype 1 / M1 GAS)
ncbi_taxonomy
Streptococcus pyogenes ATCC 700294
Streptococcus pyogenes SF370
Streptococcus pyogenes strain SF370
Streptococcus pyogenes M1 GAS
GC_ID:11
PMID:17012393
Streptococcus pyogenes Manfredo
Streptococcus pyogenes strain Manfredo
ncbi_taxonomy
Streptococcus pyogenes (serotype 5 / Manfredo)
Streptococcus pyogenes str. Manfredo
HMPV
GC_ID:1
ncbi_taxonomy
Human metapneumovirus
NCBITaxon:5072
GC_ID:1
ncbi_taxonomy
A. nidulans
Aspergillus nidulans
Aspergillus nidulellus
Aspergilus nidulans
Emericella nidulans
GC_ID:1
oriental rat flea
ncbi_taxonomy
Xenopsylla cheopis
NCBITaxon:1634566
GC_ID:11
PMID:17773427
PMID:1906732
PMID:8782698
ncbi_taxonomy
Bacterium monocytogenes
Bacterium monocytogenes hominis
Corynebacterium infantisepticum
Corynebacterium parvulum
Erysipelothrix monocytogenes
Listerella hepatolytica
Listeria momocytogenes
Lysteria monocytogenes
Listeria monocytogenes
GC_ID:11
ncbi_taxonomy
Yersinia pseudotuberculosis complex
GC_ID:11
PMID:11679669
Listeria monocytogenes EGDe
Listeria monocytogenes str. EGD-e
Listeria monocytogenes strain EGD-e
ncbi_taxonomy
Listeria monocytogenes ATCC BAA-679
Listeria monocytogenes EGD-e
GC_ID:11
PMID:11463916
ncbi_taxonomy
NCBITaxon:170187
Streptococcus pneumoniae TIGR4
NCBITaxon:29512
NCBITaxon:29514
NCBITaxon:29516
GC_ID:11
PMID:10425768
PMID:1581182
PMID:19868121
PMID:9103653
ncbi_taxonomy
Ancona
Canela
Jequitaia
Leptospira
GC_ID:11
PMID:11544234
ncbi_taxonomy
Streptococcus pneumoniae (strain ATCC BAA-255 / R6)
Streptococcus pneumoniae str. R6
NCBITaxon:171101
Streptococcus pneumoniae R6
GC_ID:11
PMID:7729671
ncbi_taxonomy
Bacillus diphtheriae
Bacterium diphtheriae
Microsporon diphthericum
Microsporon diphtheriticum
Mycobacterium diphtheriae
Pacinia loeffleri
Corynebacterium diphtheriae
GC_ID:11
PMID:1380284
PMID:1581193
PMID:16014496
PMID:1883713
PMID:2275850
PMID:29497402
PMID:7547284
PMID:7547304
PMID:7907223
PMID:8863452
ncbi_taxonomy
Mycobacterium Lehmann and Neumann 1896
Mycobacterium
GC_ID:11
PMID:2397193
PMID:8347508
ncbi_taxonomy
Bacillus tuberculosis gallinarum
Mycobacterium tuberculosis avium
Mycobacterium tuberculosis typus gallinaceus
Tuberculose des oiseaux
Mycobacterium avium
GC_ID:11
PMID:29205127
ncbi_taxonomy
Bacillus tuberculosis
Bacterium tuberculosis
Mtub-
Mycobacterium tuberculosis typus humanus
Mycobacterium tuberculosis var. hominis
NCBITaxon:1773
Mycobacterium tuberculosis
Mtub-
PRO:DAN
GC_ID:11
Francisella tularensis subsp. tularensis str. SCHU S4
Francisella tularensis subsp. tularensis strain SCHU S4
ncbi_taxonomy
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
GC_ID:1
ncbi_taxonomy
WEEV complex
GC_ID:11
PMID:18988685
PMID:23851394
ncbi_taxonomy
Terrabacteria group
NCBITaxon:427679
GC_ID:1
ncbi_taxonomy
Cryptococcus neoformans A
Cryptococcus neoformans serotype A
Filobasidiella neoformans serotype A
Filobasidiella neoformans var. grubii
Cryptococcus neoformans var. grubii
GC_ID:11
ncbi_taxonomy
Chlamydia pneumoniae TW-183
Chlamydia pneumoniae TW183
Chlamydophila pneumoniae TW183
Chlamydophila pneumoniae TW-183
GC_ID:1
ncbi_taxonomy
Trypanosoma brucei strain TREU927
NCBITaxon:185431
Trypanosoma brucei TREU927
Trypanosoma brucei brucei TREU927
GC_ID:11
PMID:11917108
ncbi_taxonomy
Streptococcus pyogenes (serotype 18 / MGAS8232)
Streptococcus pyogenes MGAS8232
ZEBOV
GC_ID:1
ncbi_taxonomy
Zaire Ebola virus
Zaire ebolavirus
GC_ID:1
ncbi_taxonomy
Clupeocephala
GC_ID:11
PMID:16558750
PMID:24480908
ncbi_taxonomy
Eubacteriales
Clostridiales
GC_ID:1
ncbi_taxonomy
Orthopneumovirus
GC_ID:11
PMID:20212322
ncbi_taxonomy
Lactobacillales
GC_ID:11
PMID:12142430
Yersinia pestis str. KIM10+
Yersinia pestis strain KIM10+
ncbi_taxonomy
Yersinia pestis KIM
Yersinia pestis KIM 10
Yersinia pestis KIM 10+
Yersinia pestis KIM10+
GC_ID:11
PMID:12712204
ncbi_taxonomy
NCBITaxon:189518
Leptospira interrogans serovar Lai str. 56601
GC_ID:11
Bacillus anthracis A2012
Bacillus anthracis strain A2012
ncbi_taxonomy
Bacillus anthracis str. A2012
GC_ID:11
PMID:10688204
Campylobacter jejuni subsp. jejuni ATCC 700819 = NCTC 11168
Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
ncbi_taxonomy
Campylobacter jejuni subsp. jejuni ATCC 700819
Campylobacter jejuni subsp. jejuni NCTC 11168
NCBITaxon:192222
Campylobacter jejuni subsp. jejuni NCTC 11168
Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
GC_ID:11
Streptococcus pyogenes str. SSI-1
ncbi_taxonomy
Streptococcus pyogenes SSI-1
GC_ID:11
PMID:15660156
PMID:16943349
Campylobacter jejuni str. RM1221
Campylobacter jejuni strain RM1221
ncbi_taxonomy
Campylobacter jejuni RM1221
GC_ID:11
PMID:11792842
Clostridium perfringens 13
ncbi_taxonomy
Clostridium perfringens str. 13
GC_ID:11
PMID:16825665
Clostridium perfringens str. ATCC 13124
Clostridium perfringens strain ATCC 13124
ncbi_taxonomy
Clostridium perfringens ATCC 13124
GC_ID:11
PMID:12044378
ncbi_taxonomy
Staphylococcus aureus (strain MW2)
Staphylococcus aureus subsp. aureus str. MW2
NCBITaxon:196620
Staphylococcus aureus subsp. aureus MW2
GC_ID:11
PMID:11321120
ncbi_taxonomy
Ampylobacter jejuni
Campylobacter fetus subsp. jejuni
Vibrio hepaticus
Vibrio jejuni
Campylobacter jejuni
Pancrustacea
Pancrustacea
ncbi_taxonomy
FluA-
NCBITaxon:197911
Influenzavirus A
FluA-
PRO:DAN
GC_ID:11
PMID:12721629
Bacillus anthracis (strain Ames)
Bacillus anthracis Ames
Bacillus anthracis strain Ames
ncbi_taxonomy
Bacillus anthracis str. Ames
GC_ID:11
PMID:12384590
ncbi_taxonomy
Shigella flexneri serotype 2a str. 301
Shigella flexneri 2a str. 301
GC_ID:11
PMID:12704152
Shigella flexneri 2a strain 2457T
Shigella flexneri serotype 2a str. 2457T
ncbi_taxonomy
Shigella flexneri 2a str. 2457T
GC_ID:11
Streptococcus pyogenes str. MGAS315
ncbi_taxonomy
Streptococcus pyogenes MGAS315
GC_ID:1
ncbi_taxonomy
Coccidioides posadasii
GC_ID:11
Escherichia coli str. CFT073
Escherichia coli strain CFT073
ncbi_taxonomy
NCBITaxon:199310
Escherichia coli CFT073
Bacteria
eubacteria
GC_ID:11
PMID:10425795
PMID:10425796
PMID:10425797
PMID:10490293
PMID:10843050
PMID:10939651
PMID:10939673
PMID:10939677
PMID:11211268
PMID:11321083
PMID:11321113
PMID:11411719
PMID:11540071
PMID:11542017
PMID:11542087
PMID:11760965
PMID:12054223
PMID:2112744
PMID:270744
PMID:8123559
PMID:8590690
PMID:9103655
PMID:9336922
Bacteria <prokaryote>
eubacteria
ncbi_taxonomy
Monera
Procaryotae
Prokaryota
Prokaryotae
bact-
bacteria
not Bacteria Haeckel 1894
prokaryote
prokaryotes
NCBITaxon:2
Bacteria
bact-
PRO:DAN
GC_ID:11
PMID:11837318
PMID:25288668
PMID:26654112
ncbi_taxonomy
Spirochaetes
Spirochaetia
GC_ID:11
PMID:12271122
Brucella suis biovar 1 (strain 1330)
Brucella suis str. 1330
ncbi_taxonomy
Brucella melitensis biovar Suis str. 1330
Brucella suis ATCC 23444
Brucella suis NCTC 10316
Bsuis1330-
NCBITaxon:204722
Brucella suis 1330
Brucella suis biovar 1 (strain 1330)
PRO:CNA
Bsuis1330-
PRO:DAN
NCBITaxon:11268
GC_ID:1
ncbi_taxonomy
Ebola virus EBO
unidentified Ebola virus
Ebola virus sp.
GC_ID:11
ncbi_taxonomy
Streptococcus agalactiae str. A909
Streptococcus agalactiae A909
GC_ID:11
PMID:12200547
Streptococcus agalactiae str. 2603V/R
ncbi_taxonomy
Streptococcus agalactiae 2603VR
NCBITaxon:208435
Streptococcus agalactiae 2603V/R
GC_ID:11
ncbi_taxonomy
Pseudomonas aeruginosa str. UCBPP-PA14
Pseudomonas aeruginosa UCBPP-PA14
GC_ID:11
PMID:10984043
ncbi_taxonomy
Pseudomonas aeruginosa PA01
Pseudomonas aeruginosa str. PA01
Pseudomonas aeruginosa str. PAO1
NCBITaxon:208964
Pseudomonas aeruginosa PAO1
GC_ID:11
PMID:12644504
Salmonella enterica subsp. enterica serovar Typhi strain Ty2
ncbi_taxonomy
Salmonella enterica subsp. enterica serovar Typhi Ty2
Salmonella enterica subsp. enterica serovar Typhi str. Ty2
GC_ID:4
ncbi_taxonomy
Mycoplasma gallisepticum
NCBITaxon:219
GC_ID:11
PMID:11931154
PMID:1995031
PMID:8186097
PMID:8494747
ncbi_taxonomy
Campylobacter pylori
Campylobacter pylori subsp. pylori
Campylobacter pyloridis
Helicobacter nemestrinae
Helicobacter pylori
NCBITaxon:11455
NCBITaxon:197769
NCBITaxon:228930
NCBITaxon:382824
NCBITaxon:384491
NCBITaxon:385648
GC_ID:1
ncbi_taxonomy
Influenza A virus ( A/Puerto Rico/8/1934(H1N1))
Influenza A virus (A/PR 8/34 (H1N1))
Influenza A virus (A/PR/8/1934(H1N1))
Influenza A virus (A/PR/8/34(H0N1))
Influenza A virus (A/PR/8/34(H1N1))
Influenza A virus (A/PR/8/34(HON1))
Influenza A virus (A/PR8/1934(H1N1))
Influenza A virus (A/Puerto Rico/8/1934(H0N1))
Influenza A virus (A/Puerto Rico/8/34(H1N1))
Influenza A virus (A/Puerto Rico/8/34)
Influenza A virus (STRAIN A/PUERTO RICO/8/34)
nfluenza A virus (A/PR 8/34(H1N1))
NCBITaxon:211044
Influenza A virus (A/Puerto Rico/8/1934(H1N1))
GC_ID:11
PMID:12354221
ncbi_taxonomy
Streptococcus agalactiae str. NEM316
Streptococcus agalactiae NEM316
GC_ID:11
PMID:12552129
ncbi_taxonomy
Clostridium tetani str. E88
NCBITaxon:212717
Clostridium tetani E88
GC_ID:11
PMID:16403855
ncbi_taxonomy
'Campylobacterales'
Campylobacterales
GC_ID:11
PMID:11586360
Yersinia pestis str. CO92
Yersinia pestis strain CO92
ncbi_taxonomy
Yersinia pestis CO92
GC_ID:1
Cryptococcus neoformans JEC21
Cryptococcus neoformans var. neoformans strain JEC21
ncbi_taxonomy
Cryptococcus neoformans var. neoformans serotype D JEC21
Filobasidiella neoformans var. neoformans strain JEC21
Cryptococcus neoformans var. neoformans JEC21
Archaea
ncbi_taxonomy
arch-
NCBITaxon:2157
Archaea
arch-
PRO:DAN
GC_ID:11
PMID:11677608
Salmonella enterica subsp. enterica serovar Typhi CT18
Salmonella enterica subsp. enterica serovar Typhi strain CT18
Salmonella typhi CT18
ncbi_taxonomy
Salmonella enterica subsp. enterica serovar Typhi str. CT18
GC_ID:11
PMID:9403685
ncbi_taxonomy
Borrelia burgdorferi str. B31
NCBITaxon:224326
Borrelia burgdorferi B31
Borreliella burgdorferi B31
GC_ID:11
PMID:11756688
Brucella melitensis biotype 1 (strain 16m / atcc 23456 / nctc 10094)
ncbi_taxonomy
Bmel16M-
Brucella melitensis 16M
Brucella melitensis ATCC 23456
Brucella melitensis str. 16M
Brucella melitensis str. ATCC 23456
NCBITaxon:224914
Brucella melitensis bv. 1 str. 16M
Brucella melitensis biotype 1 (strain 16m / atcc 23456 / nctc 10094)
PRO:CNA
Bmel16M-
PRO:DAN
GC_ID:11
PMID:12663927
Enterococcus faecalis str. V583
Enterococcus faecalis strain V583
ncbi_taxonomy
NCBITaxon:226185
Enterococcus faecalis V583
GC_ID:1
ncbi_taxonomy
Emericella nidulans FGSC A4
Aspergillus nidulans FGSC A4
GC_ID:11
PMID:12704232
ncbi_taxonomy
Coxiella burnetii str. RSA 493
NCBITaxon:227377
Coxiella burnetii RSA 493
GC_ID:11
PMID:15262951
PMID:15368893
Yersinia pestis biovar Microtus 91001
Yersinia pestis biovar Microtus strain 91001
ncbi_taxonomy
Yersinia pestis biovar Mediaevails str. 91001
Yersinia pestis biovar Medievalis str. 91001
Yersinia pestis bv. Microtus str. 91001
Yersinia pestis biovar Microtus str. 91001
GC_ID:11
PMID:28066370
PMID:8573514
ncbi_taxonomy
Bru-
Brucella Meyer and Shaw 1920
NCBITaxon:234
Brucella
Bru-
PRO:DAN
GC_ID:11
Brucella melitensis bv. Abortus
ncbi_taxonomy
Bacterium abortus
Brucella melitensis biovar Abortus
Brucella abortus
ncbi_taxonomy
NCBITaxon:235443
Cryptococcus neoformans var. grubii H99
GC_ID:12
ncbi_taxonomy
NCBITaxon:237561
Candida albicans SC5314
GC_ID:11
Burkholderia mallei str. ATCC 23344
ncbi_taxonomy
NCBITaxon:243160
Burkholderia mallei ATCC 23344
GC_ID:11
PMID:10952301
Vibrio cholerae El Tor N16961
Vibrio cholerae serotype O1 biotype El Tor strain N16961
Vibrio cholerae serotype O1 biotype ElTor strain N16961
ncbi_taxonomy
Vchol-
Vibrio cholerae O1 biovar eltor str. N16961
NCBITaxon:243277
Vibrio cholerae O1 biovar El Tor str. N16961
Vchol-
PRO:DAN
GC_ID:11
PMID:14602910
Corynebacterium diphtheriae NCTC13129
ncbi_taxonomy
Corynebacterium diphtheriae NCTC 13129
GC_ID:11
PMID:12910271
ncbi_taxonomy
Bordetella bronchiseptica RB50
GC_ID:11
PMID:12910271
ncbi_taxonomy
NCBITaxon:257313
Bordetella pertussis Tohama I
GC_ID:11
Bacillus anthracis (strain Sterne)
Bacillus anthracis Sterne
ncbi_taxonomy
Bacillus anthracis str. Sterne
GC_ID:11
PMID:18952800
Bacillus anthracis Ames "Ancestor"
Bacillus anthracis str. Ames Ancestor
Bacillus anthracis strain 'Ames Ancestor'
ncbi_taxonomy
Bacillus anthracis str. Ames 0581
Bacillus anthracis str. 'Ames Ancestor'
NCBITaxon:164623
OpMNPV
GC_ID:1
ncbi_taxonomy
Orgya pseudotsugata MNPV
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
Orgyia pseudotsugata MNPV
GC_ID:11
PMID:16116077
PMID:20870759
Mycobacterium avium subsp. paratuberculosis str. K-10
Mycobacterium avium subsp. paratuberculosis strain K-10
ncbi_taxonomy
Mycobacterium avium subsp. paratuberculosis K10
Mycobacterium avium subsp. paratuberculosis K-10
GC_ID:11
ncbi_taxonomy
Bacterium tularense
Brucella tularensis
Francisella tularense
Pasteurella tularensis
Francisella tularensis
GC_ID:11
Listeria monocytogenes serotype 4b strain F2365
ncbi_taxonomy
Listeria monocytogenes str. 4b F2365
Listeria monocytogenes serotype 4b str. F2365
GC_ID:1
ncbi_taxonomy
Pneumonia virus of mice J3666
NCBITaxon:10458
BmNPV
BmSNPV
GC_ID:1
ncbi_taxonomy
Bombyx mori S nuclear polyhedrosis virus
Bombyx mori nuclear polyhedrosis virus
Bombyx mori nuclear polyhedrosis virus BmNPV
Bombyx mori nuclear polyhedrosis virus, BmSNPV
Bombyx mori nucleopolyhedrosis virus
Bombyx mori nucleopolyhedrovirus
Bombyx mori NPV
GC_ID:11
Burkholderia pseudomallei str. K96243
Burkholderia pseudomallei strain K96243
ncbi_taxonomy
NCBITaxon:272560
Burkholderia pseudomallei K96243
GC_ID:11
Chlamydia trachomatis str. D/UW-3/CX
Chlamydia trachomatis strain D/UW-3/CX
ncbi_taxonomy
NCBITaxon:272561
Chlamydia trachomatis D/UW-3/CX
GC_ID:11
Clostridium difficile 630 (epidemic type X)
Clostridium difficile str. 630
Clostridium difficile strain 630
ncbi_taxonomy
NCBITaxon:272563
Clostridioides difficile 630
Clostridium difficile 630
GC_ID:11
PMID:15448271
Legionella pneumophila subsp. pneumophila 'Philadelphia 1'
Legionella pneumophila subsp. pneumophila strain Philadelphia 1
ncbi_taxonomy
Legionella pneumophila subsp. pneumophila str. Philadelphia 1
GC_ID:11
Neisseria meningitidis str. FAM18
Neisseria meningitidis strain FAM18
ncbi_taxonomy
Neisseria meningitidis FAM18
GC_ID:11
Pasteurella multocida subsp. multocida Pm70
Pasteurella multocida subsp. multocida strain Pm70
ncbi_taxonomy
Pasteurella multocida subsp. multocida str. Pm70
GC_ID:11
PMID:9823893
Rickettsia prowazekii 'Madrid E'
Rickettsia prowazekii strain Madrid E
ncbi_taxonomy
Rickettsia prowazekii str. Madrid E
GC_ID:11
Staphylococcus aureus str. RF122
Staphylococcus aureus strain RF122
ncbi_taxonomy
NCBITaxon:273036
Staphylococcus aureus RF122
GC_ID:11
Yersinia pseudotuberculosis IP32953
Yersinia pseudotuberculosis str. IP 32953
Yersinia pseudotuberculosis strain IP 32953
ncbi_taxonomy
NCBITaxon:273123
Yersinia pseudotuberculosis IP 32953
Eukaryota
eucaryotes
eukaryotes
GC_ID:1
PMID:23020233
eucaryotes
eukaryotes
ncbi_taxonomy
Eucarya
Eucaryotae
Eukarya
Eukaryotae
euk-
eukaryotes
NCBITaxon:2759
Eukaryota
euk-
PRO:DAN
GC_ID:11
PMID:15968074
Haemophilus influenzae str. 86-028NP
Haemophilus influenzae strain 86-028NP
ncbi_taxonomy
Haemophilus influenzae 86-028NP
GC_ID:11
PMID:11541974
PMID:11837318
PMID:16166687
PMID:16403855
PMID:19060069
ncbi_taxonomy
"Alphabacteria" Cavalier-Smith 1992
Alphabacteria
Alphabacteria Cavalier-Smith 2002
Alphaproteobacteria Garrity et al. 2006
Proteobacteria alpha subdivision
Purple bacteria, alpha subdivision
a-proteobacteria
alpha proteobacteria
alpha subdivision
alpha subgroup
Alphaproteobacteria
GC_ID:11
PMID:16403855
PMID:28581923
ncbi_taxonomy
'Betaproteobacteria'
Proteobacteria beta subdivision
Purple bacteria, beta subdivision
b-proteobacteria
beta proteobacteria
beta subdivision
beta subgroup
Betaproteobacteria
GC_ID:11
PMID:15213324
Staphylococcus aureus subsp. aureus str. MRSA252
Staphylococcus aureus subsp. aureus strain MRSA252
ncbi_taxonomy
NCBITaxon:282458
Staphylococcus aureus subsp. aureus MRSA252
GC_ID:11
PMID:15210978
Bartonella henselae strain Houston-1
ncbi_taxonomy
Bartonella henselae ATCC 49882
Bartonella henselae str. ATCC 49882
Bartonella henselae strain ATCC 49882
Bartonella henselae str. Houston-1
NCBITaxon:12796
NCBITaxon:70172
PRRSV
GC_ID:1
ncbi_taxonomy
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
GC_ID:1
ncbi_taxonomy
NCBITaxon:283643
Cryptococcus neoformans var. neoformans B-3501A
GC_ID:1
ncbi_taxonomy
Influenza A virus (A/Vietnam/1203/04(H5N1))
Influenza A virus (A/Vietnam/1203/2004)
Influenza A virus (A/Viet Nam/1203/2004(H5N1))
NCBITaxon:1435366
NCBITaxon:1435368
NCBITaxon:1435988
NCBITaxon:1439853
NCBITaxon:1487954
NCBITaxon:1487955
GC_ID:11
PMID:12734250
PMID:1283774
ncbi_taxonomy
Bacillus pseudomallei
Bacterium whitmori
Burkholderia pseudomallai
Burkholderia pseudomallei MSHR4009
Burkholderia pseudomallei MSHR4018
Burkholderia pseudomallei MSHR44
Burkholderia pseudomallei MSHR7839
Burkholderia sp. MSHR7839
Loefflerella pseudomallei
Malleomyces pseudomallei
Pseudomonas pseudomallei
Burkholderia pseudomallei
GC_ID:1
Candida glabrata ATCC 2001
Candida glabrata ATCC2001
Candida glabrata CBS138
ncbi_taxonomy
Candida glabrata CBS 138
GC_ID:1
ncbi_taxonomy
Eurotiaceae
Trichocomaceae
GC_ID:11
PMID:15272401
Streptococcus pyogenes str. MGAS10394
Streptococcus pyogenes strain MGAS10394
ncbi_taxonomy
Streptococcus pyogenes MGAS10394
NCBITaxon:1224290
NCBITaxon:1437768
NCBITaxon:1437769
NCBITaxon:1437770
NCBITaxon:1508364
NCBITaxon:1683559
NCBITaxon:1683561
NCBITaxon:1851858
NCBITaxon:1851865
NCBITaxon:1860124
NCBITaxon:665948
NCBITaxon:931955
NCBITaxon:931956
NCBITaxon:931957
NCBITaxon:931958
NCBITaxon:932477
GC_ID:11
ncbi_taxonomy
Bacillus aeruginosus
Bacillus pyocyaneus
Bacterium aeruginosum
Bacterium pyocyaneum
Micrococcus pyocyaneus
Peudomonas aeruginosa
Pseudomonas polycolor
Pseudomonas pyocyanea
Pseudomonas sp. 2_1_26
probable synonym or variety: "Pseudomonas polycolor" Clara 1930
NCBITaxon:287
Pseudomonas aeruginosa
NCBITaxon:10973
NCBITaxon:183404
GC_ID:1
ncbi_taxonomy
Group A rotaviruses
Rotavirus group A
group A rotavirus
Rotavirus A
GC_ID:11
PMID:16825665
Clostridium perfringens str. SM101
Clostridium perfringens strain SM101
ncbi_taxonomy
Clostridium perfringens SM101
GC_ID:11
ncbi_taxonomy
Streptococcus pyogenes MGAS5005
GC_ID:1
ncbi_taxonomy
Entamoeba histolytica HM-1:IMSS
GC_ID:11
PMID:8573514
ncbi_taxonomy
Micrococcus melitensis
Streptococcus Miletensis
Brucella melitensis
GC_ID:11
ncbi_taxonomy
Yersinia ruckeri
GC_ID:11
ncbi_taxonomy
Salmonella enterica subsp. enterica serovar Paratypi A str. ATCC 9150
Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
GC_ID:11
ncbi_taxonomy
Legionella pneumophila Lens
Legionella pneumophila str. Lens
GC_ID:11
ncbi_taxonomy
Legionella pneumophila Paris
Legionella pneumophila str. Paris
GC_ID:11
Shigella dysenteriae str. Sd197
Shigella dysenteriae strain Sd197
ncbi_taxonomy
NCBITaxon:300267
Shigella dysenteriae Sd197
GC_ID:11
Shigella boydii str. Sb227
Shigella boydii strain Sb227
ncbi_taxonomy
Shigella boydii Sb227
GC_ID:11
Shigella sonnei str. Ss046
Shigella sonnei strain Ss046
ncbi_taxonomy
Shigella sonnei Ss046
GC_ID:11
ncbi_taxonomy
NCBITaxon:301447
Streptococcus pyogenes serotype M1
GC_ID:11
Streptococcus pyogenes (serotype M3)
ncbi_taxonomy
Streptococcus pyogenes serotype M3
GC_ID:1
PMID:11214318
PMID:11214319
PMID:12878460
ncbi_taxonomy
Laurasiatheria
Euarchontoglires
GC_ID:1
PMID:11214319
PMID:12082125
PMID:12878460
PMID:15522813
ncbi_taxonomy
Euarchontoglires
GC_ID:1
PMID:11214319
PMID:12082125
PMID:15522813
Rodents and rabbits
ncbi_taxonomy
Glires
GC_ID:1
ncbi_taxonomy
Anthropoidea
Simiiformes
GC_ID:11
PMID:18245285
Escherichia coli DH10B
Escherichia coli str. K12 substr. DH10B
Escherichia coli strain K12 substrain DH10B
ncbi_taxonomy
Escherichia coli str. K-12 substr. DH10B
GC_ID:11
PMID:20802035
Escherichia coli ETEC str. H10407
Escherichia coli ETEC strain H10407
ncbi_taxonomy
Escherichia coli H10407
Escherichia coli strain H10407
Escherichia coli ETEC H10407
GC_ID:11
Streptococcus pyogenes str. MGAS6180
Streptococcus pyogenes strain MGAS6180
ncbi_taxonomy
Streptococcus pyogenes MGAS6180
GC_ID:11
PMID:11321120
Campylobacter jejuni jejuni
ncbi_taxonomy
Campylobacter jejuni subsp. jejuni
GC_ID:11
Burkholderia pseudomallei str. 1710b
Burkholderia pseudomallei strain 1710b
ncbi_taxonomy
Burkholderia pseudomallei 1710b
GC_ID:11
Burkholderia pseudomallei str. 668
Burkholderia pseudomallei strain 668
ncbi_taxonomy
Burkholderia pseudomallei 668
GC_ID:11
Burkholderia mallei str. SAVP1
Burkholderia mallei strain SAVP1
ncbi_taxonomy
Burkholderia mallei SAVP1
GC_ID:11
Burkholderia mallei str. NCTC 10247
Burkholderia mallei strain NCTC 10247
ncbi_taxonomy
Burkholderia mallei NCTC 10247
GC_ID:11
Salmonella enterica subsp. enterica serovar Choleraesuis SC-B67
Salmonella enterica subsp. enterica serovar Choleraesuis strain SC-B67
ncbi_taxonomy
Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
Tetrapoda
tetrapods
Tetrapoda
Amniota
amniotes
GC_ID:1
amniotes
ncbi_taxonomy
Amniota
GC_ID:1
ncbi_taxonomy
NCBITaxon:330879
Aspergillus fumigatus Af293
ncbi_taxonomy
plant-
NCBITaxon:33090
Viridiplantae
plant-
PRO:DAN
GC_ID:11
PMID:18676672
Escherichia coli str. E24377A
Escherichia coli strain E24377A
ncbi_taxonomy
Escherichia coli E24377A
GC_ID:11
PMID:18676672
Escherichia coli str. HS
Escherichia coli strain HS
ncbi_taxonomy
Escherichia coli HS
Opisthokonta
GC_ID:1
ncbi_taxonomy
Fungi/Metazoa group
opisthokonts
NCBITaxon:33154
Opisthokonta
NCBITaxon:259362
NCBITaxon:36053
NCBITaxon:5102
GC_ID:1
PMID:17486980
ncbi_taxonomy
Gymnoascales
Onygenales
ncbi_taxonomy
metazoan-
NCBITaxon:33208
Metazoa
metazoan-
PRO:DAN
Bilateria
GC_ID:1
ncbi_taxonomy
Bilateria
GC_ID:1
ncbi_taxonomy
Endopterygota
Holometabola
GC_ID:11
Mycobacterium tuberculosis str. F11
Mycobacterium tuberculosis strain F11
ncbi_taxonomy
Mycobacterium tuberculosis F11
NCBITaxon:10348
GC_ID:1
ncbi_taxonomy
Pseudorabies virus (STRAIN KA)
Pseudorabies virus (strain Kaplan)
Suid herpesvirus 1 (strain KA)
Suid herpesvirus 1 (strain Kaplan)
Suid herpesvirus 1 strain Kaplan
GC_ID:1
PMID:15019624
PMID:15371245
ncbi_taxonomy
Muroidea
GC_ID:11
ncbi_taxonomy
Actinobacillus pleuropneumoniae 2
Actinobacillus pleuropneumoniae serotype 2
Actinobacillus pleuropneumoniae serovar 2
GC_ID:11
ncbi_taxonomy
Streptococcus pyogenes serotype M12
GC_ID:11
Shigella boydii str. CDC 3083-94
Shigella boydii strain CDC 3083-94
ncbi_taxonomy
Shigella boydii BS512
Shigella boydii CDC 3083-94
GC_ID:1
ncbi_taxonomy
SARS coronavirus ZJ0301
GC_ID:11
Vibrio cholerae str. O395
Vibrio cholerae strain O395
ncbi_taxonomy
Vibrio cholerae O395
LmjF
GC_ID:1
ncbi_taxonomy
Leishmania major MHOM/IL/81/Friedlin
Leishmania major strain Friedlin
GC_ID:11
PMID:20061468
Yersinia pestis str. Angola
Yersinia pestis strain Angola
ncbi_taxonomy
Yersinia pestis Angola O.Pe.3
Yersinia pestis Angola
GC_ID:11
Yersinia pseudotuberculosis str. IP 31758
Yersinia pseudotuberculosis strain IP 31758
ncbi_taxonomy
Yersinia pseudotuberculosis IP 31758
GC_ID:1
ncbi_taxonomy
dsDNA viruses
dsDNA viruses, no RNA stage
NCBITaxon:12593
NCBITaxon:36349
BoHV-5
GC_ID:1
ncbi_taxonomy
Bovine encephalitis herpesvirus
Bovine herpesvirus type 5
Bovine herpesvirus 5
Retro-transcribing viruses
Retro-transcribing viruses
GC_ID:1
ncbi_taxonomy
ssRNA positive-strand viruses, no DNA stage
GC_ID:1
ncbi_taxonomy
Plasmodium yoelii yoelii str. 17XNL
Plasmodium yoelii yoelii 17XNL
GC_ID:1
ncbi_taxonomy
ssRNA negative-strand viruses
GC_ID:1
ncbi_taxonomy
Cryptosporidium parvum strain Iowa type II
Cryptosporidium parvum Iowa II
GC_ID:1
ncbi_taxonomy
NCBITaxon:353153
Trypanosoma cruzi strain CL Brener
GC_ID:11
Campylobacter jejuni subsp. jejuni str. 81-176
Campylobacter jejuni subsp. jejuni strain 81-176
ncbi_taxonomy
Campylobacter jejuni subsp. jejuni 81-176
GC_ID:11
PMID:16403855
PMID:1854635
rhizobacteria
ncbi_taxonomy
'Rhizobiales'
Rhizobiaceae group
alpha-2 proteobacteria
Rhizobiales
GC_ID:1
ncbi_taxonomy
Dictyochales
GC_ID:11
Burkholderia pseudomallei str. 1106a
Burkholderia pseudomallei strain 1106a
ncbi_taxonomy
Burkholderia pseudomallei 1106a
GC_ID:11
PMID:16299333
PMID:20462421
Brucella melitensis biovar Abortus str. 2308
Brucella melitensis biovar Abortus strain 2308
ncbi_taxonomy
BmelAbo2308-
NCBITaxon:359391
Brucella abortus 2308
Brucella melitensis biovar Abortus 2308
BmelAbo2308-
PRO:DAN
GC_ID:11
Bartonella bacilliformis str. KC583
Bartonella bacilliformis strain KC583
ncbi_taxonomy
Bartonella bacilliformis KC583
GC_ID:11
Yersinia pestis str. Antiqua
Yersinia pestis strain Antiqua
ncbi_taxonomy
Yersinia pestis Antiqua
GC_ID:11
Campylobacter jejuni subsp. doylei str. 269.97
Campylobacter jejuni subsp. doylei strain 269.97
ncbi_taxonomy
Campylobacter jejuni subsp. doylei 362.97
Campylobacter jejuni subsp. doylei 269.97
GC_ID:11
Bordetella avium str. 197N
Bordetella avium strain 197N
ncbi_taxonomy
Bordetella avium 197N
GC_ID:11
PMID:16912116
Escherichia coli str. 536
Escherichia coli strain 536
ncbi_taxonomy
Escherichia coli 536
GC_ID:1
ncbi_taxonomy
PLASMODIUM FALCIPARUM (ISOLATE 3D7).
Plasmodium falciparum (isolate 3D7)
NCBITaxon:36329
Plasmodium falciparum 3D7
GC_ID:11
Escherichia coli str. UTI89
Escherichia coli strain UTI89
ncbi_taxonomy
Escherichia coli UTI89
NCBITaxon:10977
NCBITaxon:28878
GC_ID:1
ncbi_taxonomy
Group C rotaviruses
Rotavirus group C
group C rotavirus
Rotavirus C
NCBITaxon:381766
NCBITaxon:548158
GC_ID:1
Cryptococcus bacillisporus VGI WM276
Cryptococcus bacillisporus WM276
Cryptococcus neoformans WM276
ncbi_taxonomy
Cryptococcus gattii WM276
GC_ID:11
PMID:8863443
ncbi_taxonomy
Clostridium botulinum A
GC_ID:11
PMID:16636287
Streptococcus pyogenes str. MGAS9429
Streptococcus pyogenes strain MGAS9429
ncbi_taxonomy
Streptococcus pyogenes MGAS9429
GC_ID:11
PMID:16636287
Streptococcus pyogenes str. MGAS10270
Streptococcus pyogenes strain MGAS10270
ncbi_taxonomy
Streptococcus pyogenes MGAS10270
GC_ID:11
PMID:16636287
Streptococcus pyogenes str. MGAS2096
Streptococcus pyogenes strain MGAS2096
ncbi_taxonomy
Streptococcus pyogenes MGAS2096
GC_ID:11
PMID:16636287
Streptococcus pyogenes str. MGAS10750
Streptococcus pyogenes strain MGAS10750
ncbi_taxonomy
Streptococcus pyogenes MGAS10750
GC_ID:11
Streptococcus pneumoniae str. D39
Streptococcus pneumoniae strain D39
ncbi_taxonomy
NCBITaxon:373153
Streptococcus pneumoniae D39
GC_ID:11
PMID:16822325
ncbi_taxonomy
Shigella flexneri 5 strain 8401
Shigella flexneri 5 str. 8401
GC_ID:11
Neisseria meningitidis str. 053442
Neisseria meningitidis strain 053442
ncbi_taxonomy
Neisseria meningitidis 053442
GC_ID:11
Francisella tularensis subsp. holarctica str. LVS
Francisella tularensis subsp. holarctica strain LVS
ncbi_taxonomy
Francisella tularensis subsp. holarctica LVS
GC_ID:11
ncbi_taxonomy
Escherichia coli O26:H-
GC_ID:11
Yersinia pestis str. Nepal516
Yersinia pestis strain Nepal516
ncbi_taxonomy
Yersinia pestis Nepal516
GC_ID:11
PMID:18801193
Aeromonas salmonicida subsp. salmonicida str. A449
Aeromonas salmonicida subsp. salmonicida strain A449
ncbi_taxonomy
Aeromonas salmonicida subsp. salmonicida A449
GC_ID:11
Bartonella tribocorum str. CIP 105476
Bartonella tribocorum strain CIP 105476
ncbi_taxonomy
Bartonella tribocorum CIP 105476
NCBITaxon:806
GC_ID:11
PMID:1371515
PMID:8240958
ncbi_taxonomy
Rochalimaea henselae
Bartonella henselae
GC_ID:1
Leishmania
ncbi_taxonomy
Leishmania <subgenus>
GC_ID:1
ncbi_taxonomy
Leishmania donovani species complex
GC_ID:11
Escherichia coli O157:H7 strain Sakai
ncbi_taxonomy
Escherichia coli O157:H7 str. Sakai
GC_ID:11
PMID:17966401
Yersinia pestis str. Pestoides F
Yersinia pestis strain Pestoides F
ncbi_taxonomy
Yersinia pestis Pestoides F
NCBITaxon:56147
GC_ID:1
alfalfa
lucerne
ncbi_taxonomy
Medicago sativa subsp. sativa
alfalfa
NCBITaxon:3879
Medicago sativa
alfalfa
Murinae
NCBITaxon:109679
GC_ID:1
ncbi_taxonomy
Murinae
GC_ID:11
Yersinia enterocolitica subsp. enterocolitica str. 8081
Yersinia enterocolitica subsp. enterocolitica strain 8081
ncbi_taxonomy
NCBITaxon:393305
Yersinia enterocolitica subsp. enterocolitica 8081
GC_ID:1
ncbi_taxonomy
Circoviridae
GC_ID:11
Legionella pneumophila 'Corby'
Legionella pneumophila strain Corby
ncbi_taxonomy
Legionella pneumophila str. Corby
NCBITaxon:135857
GC_ID:1
ncbi_taxonomy
Cryptococcus neoformans serotype D
Filobasidiella neoformans var. neoformans
Cryptococcus neoformans var. neoformans
GC_ID:11
PMID:17293413
Escherichia coli str. APEC O1
Escherichia coli strain APEC O1
ncbi_taxonomy
Escherichia coli APEC O1
Mammalia
mammals
mammal
ncbi_taxonomy
mammal-
NCBITaxon:40674
Mammalia
mammal
mammal-
PRO:DAN
GC_ID:11
PMID:17873037
Campylobacter jejuni subsp. jejuni str. 81116
Campylobacter jejuni subsp. jejuni strain 81116
ncbi_taxonomy
Campylobacter jejuni subsp. jejuni NCTC 11828
Campylobacter jejuni subsp. jejuni 81116
GC_ID:11
Escherichia coli str. SE11
Escherichia coli strain SE11
ncbi_taxonomy
Escherichia coli SE11
NCBITaxon:320386
GC_ID:11
Burkholderia mallei str. 10229
Burkholderia mallei strain 10229
ncbi_taxonomy
Burkholderia mallei 10229
Burkholderia mallei NCTC 10229
GC_ID:11
Yersinia pestis str. CA88-4125
Yersinia pestis strain CA88-4125
ncbi_taxonomy
Yersinia pestis CA88-4125
GC_ID:11
Escherichia coli B (REL606 strain)
Escherichia coli B strain REL606
Escherichia coli str. B substr. REL606
ncbi_taxonomy
Escherichia coli B str. Bc251
Escherichia coli B str. REL606
GC_ID:11
PMID:18065534
Actinobacillus pleuropneumoniae serovar 5b strain L20
ncbi_taxonomy
Actinobacillus pleuropneumoniae L20
Actinobacillus pleuropneumoniae serovar 5b str. L20
GC_ID:1
ncbi_taxonomy
Vinckeia
Plasmodium (Vinckeia)
GC_ID:11
Staphylococcus aureus subsp. aureus str. Mu3
Staphylococcus aureus subsp. aureus strain Mu3
ncbi_taxonomy
NCBITaxon:418127
Staphylococcus aureus subsp. aureus Mu3
GC_ID:11
Mycobacterium tuberculosis str. H37Ra
Mycobacterium tuberculosis strain H37Ra
ncbi_taxonomy
Mycobacterium tuberculosis ATCC 25177
Mycobacterium tuberculosis H37Ra
GC_ID:1
ncbi_taxonomy
Eimeriorina
GC_ID:11
Legionella pneumophila str. 2300/99 Alcoy
Legionella pneumophila strain 2300/99 Alcoy
ncbi_taxonomy
Legionella pneumophila 2300/99
Legionella pneumophila 2300/99 Alcoy
GC_ID:12
ncbi_taxonomy
Candida dubliniensis
GC_ID:11
PMID:17951380
Staphylococcus aureus subsp. aureus strain Newman
ncbi_taxonomy
Staphylococcus aureus subsp. aureus Newman
NCBITaxon:426430
Staphylococcus aureus subsp. aureus str. Newman
GC_ID:11
ncbi_taxonomy
Shigella flexneri serotype 2a
Shigella flexneri 2a
GC_ID:11
ncbi_taxonomy
Actinobacillus pleuropneumoniae serovar 3 str. JL03
GC_ID:1
ncbi_taxonomy
ssRNA viruses
GC_ID:11
PMID:18708504
Escherichia coli str. SMS-3-5
Escherichia coli strain SMS-3-5
ncbi_taxonomy
Escherichia coli SECEC SMS-3-5
Escherichia coli SMS-3-5
GC_ID:11
Clostridium botulinum A ATCC 19397
Clostridium botulinum A strain ATCC 19397
ncbi_taxonomy
Clostridium botulinum A str. ATCC 19397
GC_ID:11
Clostridium botulinum A strain Hall
ncbi_taxonomy
NCBITaxon:441771
Clostridium botulinum A str. Hall
GC_ID:11
ncbi_taxonomy
Escherichia coli O157:H7 str. EC4115
GC_ID:11
PMID:20935092
Borrelia burgdorferi str. 156a
Borrelia burgdorferi strain 156a
ncbi_taxonomy
Borrelia burgdorferi 156a
GC_ID:11
PMID:20935092
Borrelia burgdorferi str. ZS7
Borrelia burgdorferi strain ZS7
ncbi_taxonomy
Borrelia burgdorferi ZS7
GC_ID:11
PMID:434652
ncbi_taxonomy
Legionella pneumophila
Dictyostelium discoideum
GC_ID:1
slime mold
ncbi_taxonomy
NCBITaxon:44689
Dictyostelium discoideum
slime mold
GC_ID:1
PMID:15689432
PMID:16151185
PMID:17010206
PMID:17051209
PMID:17572334
ncbi_taxonomy
Dikarya
GC_ID:1
ncbi_taxonomy
Eurotiomycetidae
GC_ID:11
Francisella tularensis subsp. holarctica str. FTNF002-00
Francisella tularensis subsp. holarctica strain FTNF002-00
ncbi_taxonomy
Francisella tularensis subsp. holarctica FTA
Francisella tularensis subsp. holarctica FTNF002-00
GC_ID:11
ncbi_taxonomy
Vibrio cholerae O139 strain
Vibrio cholerae serogroup O139
Vibrio cholerae O139
NCBITaxon:10446
AcMNPV
GC_ID:1
ncbi_taxonomy
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
GC_ID:11
Staphylococcus aureus aureus
ncbi_taxonomy
Staphylococcus aureus subsp. aureus
GC_ID:11
PMID:18820018
Streptococcus pyogenes str. NZ131
Streptococcus pyogenes strain NZ131
ncbi_taxonomy
Streptococcus pyogenes NZ131
GC_ID:11
Enterococcus faecalis str. OG1RF
Enterococcus faecalis strain OG1RF
ncbi_taxonomy
Enterococcus faecalis OG1RF
ncbi_taxonomy
fungal-
NCBITaxon:4751
Fungi
fungal-
PRO:DAN
GC_ID:11
Salmonella enterica subsp. enterica serovar Paratyphi C str. RKS4594
ncbi_taxonomy
Salmonella paratyphi C str. RKS4594
Salmonella paratyphi C strain RKS4594
Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
GC_ID:11
ncbi_taxonomy
Geobacillus sp. Y412MC10
Paenibacillus sp. Y412MC10
GC_ID:11
ncbi_taxonomy
Diplokokkus intracellularis meningitidis
Micrococcus intracellularis
Micrococcus meningitidis
Micrococcus meningitidis cerebrospinalis
Neisseria meningitidis.
Neisseria weichselbaumii
Neisseria meningitidis
GC_ID:11
Streptococcus pneumoniae str. Taiwan19F-14
Streptococcus pneumoniae strain Taiwan19F-14
ncbi_taxonomy
Streptococcus pneumoniae Taiwan19F-14
GC_ID:11
Streptococcus pneumoniae str. Hungary19A-6
Streptococcus pneumoniae strain Hungary19A-6
ncbi_taxonomy
Streptococcus pneumoniae Hungary19A-6
GC_ID:11
Streptococcus pneumoniae str. 70585
Streptococcus pneumoniae strain 70585
ncbi_taxonomy
Streptococcus pneumoniae 70585
GC_ID:11
Streptococcus pneumoniae str. JJA
Streptococcus pneumoniae strain JJA
ncbi_taxonomy
Streptococcus pneumoniae JJA
GC_ID:11
Streptococcus pneumoniae str. P1031
Streptococcus pneumoniae strain P1031
ncbi_taxonomy
Streptococcus pneumoniae P1031
Ascomycota
ascomycetes
sac fungi
Ascomycota
GC_ID:1
budding yeasts
ncbi_taxonomy
Endomycetales
Saccharomycetales
NCBITaxon:221665
NCBITaxon:44280
GC_ID:1
ncbi_taxonomy
Saccharomycetaceae
Saccharomyces cerevisiae
baker's yeast
brewer's yeast
lager beer yeast
yeast
GC_ID:1
baker's yeast
brewer's yeast
lager beer yeast
yeast
ncbi_taxonomy
Candida robusta
Saccaromyces cerevisiae
Saccharomyce cerevisiae
Saccharomyces capensis
Saccharomyces italicus
Saccharomyces oviformis
Saccharomyces uvarum var. melibiosus
Saccharomyes cerevisiae
Sccharomyces cerevisiae
NCBITaxon:4932
Saccharomyces cerevisiae
GC_ID:11
Clostridium botulinum B1 strain Okra
ncbi_taxonomy
Clostridium botulinum B1 str. Okra
GC_ID:11
Clostridium botulinum A3 strain Loch Maree
ncbi_taxonomy
Clostridium botulinum A3 str. Loch Maree
GC_ID:11
Edwardsiella tarda str. EIB202
Edwardsiella tarda strain EIB202
ncbi_taxonomy
Edwardsiella tarda EIB202
GC_ID:11
Yersinia pseudotuberculosis str. YPIII
Yersinia pseudotuberculosis strain YPIII
ncbi_taxonomy
Yersinia pseudotuberculosis YPIII
GC_ID:11
Yersinia pseudotuberculosis str. PB1/+
Yersinia pseudotuberculosis strain PB1/+
ncbi_taxonomy
Yersinia pseudotuberculosis PB1/+
NCBITaxon:61255
GC_ID:1
ncbi_taxonomy
Ajellomyces capsulata
Ajellomyces capsulatas
Ajellomyces capsulatus
Cryptococcus capsulatus
Emmonsiella capsulata
Histoplasma capsulatum
Ajellomyces capsulatus
Histoplasma capsulatum
GC_ID:1
trouts, salmons & chars
ncbi_taxonomy
Salmoninae
GC_ID:11
Clostridium botulinum E3 strain Alaska E43
ncbi_taxonomy
Clostridium botulinum E3 str. Alaska E43
GC_ID:1
ncbi_taxonomy
Toxoplasma gondii strain ME49
Toxoplasma gondii ME49
GC_ID:11
Escherichia coli str. K12 substr. MG1655
Escherichia coli str. MG1655
Escherichia coli strain MG1655
ncbi_taxonomy
Escherichia coli MG1655
Escherichia coli str. K-12 substr. MG1655
GC_ID:11
Streptococcus pneumoniae str. G54
Streptococcus pneumoniae strain G54
ncbi_taxonomy
Streptococcus pneumoniae G54
GC_ID:11
Streptococcus pneumoniae str. CGSP14
Streptococcus pneumoniae strain CGSP14
ncbi_taxonomy
Streptococcus pneumoniae CGSP14
GC_ID:11
PMID:11491321
ncbi_taxonomy
Bordetella Moreno-Lopez 1952 (Approved Lists 1980) emend. Von Wintzingerode et al. 2001
Bordetella
NCBITaxon:514
GC_ID:11
PMID:8240949
PMID:8782670
PMID:9226899
ncbi_taxonomy
Alcaligenes bronchicanis
Alcaligenes bronchisepticus
Bacillus bronchicanis
Bacillus bronchisepticus
Bacterium bronchisepticus
Bordetella bronchiseptica@
Brucella bronchiseptica
Brucella bronchispetica
Haemophilus bronchisepticus
Bordetella bronchiseptica
GC_ID:11
PMID:8240949
ncbi_taxonomy
Bacterium tussis-convulsivae
Haemophilus pertussis
Hemophilus pertussis
Microbe de la coqueluche
Bordetella pertussis
NCBITaxon:107441
NCBITaxon:192653
NCBITaxon:5415
GC_ID:1
Cryptococcus
ncbi_taxonomy
Filobasidiella
Cryptococcus <basidiomycete yeast>
GC_ID:1
ncbi_taxonomy
Blastomyces neoformans
Debaryomyces neoformans
Filobasidiella neoformans
Filobasidiella neoformornans
Filobaxidiella neoformans
Lipomyces neoformans
Saccharomyces neoformans
Torula neoformans
Torulopsis neoformans
Cryptococcus neoformans
GC_ID:11
PMID:4074238
ncbi_taxonomy
Bordetella avium
GC_ID:11
PMID:20935092
Borrelia burgdorferi str. N40
Borrelia burgdorferi strain N40
ncbi_taxonomy
Borrelia burgdorferi N40
GC_ID:11
PMID:20935092
Borrelia burgdorferi str. 297
Borrelia burgdorferi strain 297
ncbi_taxonomy
Borrelia burgdorferi 297
GC_ID:1
Hymenomycetes
ncbi_taxonomy
Agaricomycotina
GC_ID:11
Burkholderia pseudomallei str. MSHR346
Burkholderia pseudomallei strain MSHR346
ncbi_taxonomy
Burkholderia pseudomallei MSHR346
GC_ID:11
Actinobacillus pleuropneumoniae serovar 7 strain AP76
ncbi_taxonomy
Actinobacillus pleuropneumoniae serovar 7 str. AP76
GC_ID:11
PMID:10555323
PMID:10555334
PMID:16166704
PMID:27620848
ncbi_taxonomy
Enterobacteraceae
Enterobacteraceae (ex Lapage 1979) Lapage 1982, fam. nov., nom. rev.
Enterobacteriaceae (ex Rahn 1937) Ewing et al. 1980, fam. nov., nom. rev.
Enterobacteriaceae Rahn 1937
gamma-3 proteobacteria
Enterobacteriaceae
GC_ID:11
Escherichia coli O157:H7 strain TW14359
ncbi_taxonomy
Escherichia coli O157:H7 str. TW14359
GC_ID:1
ncbi_taxonomy
Torulopsis
Candida
NCBITaxon:39399
GC_ID:12
ncbi_taxonomy
Candida albican
Candida stellatoidea
Candida stellatoidea type I
Candida albicans
GC_ID:1
PMID:14654427
Candida glabrata
ncbi_taxonomy
Candidia glabrata
Cryptococcus glabratus
Torulopsis glabrata
Candida glabrata
[Candida] glabrata
GC_ID:1
ncbi_taxonomy
Coccidioides
GC_ID:11
Salmonella enterica subsp. enterica serovar Enteritidis strain P125109
ncbi_taxonomy
Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
GC_ID:11
Salmonella enterica subsp. enterica serovar Gallinarum strain 287/91
ncbi_taxonomy
Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91
GC_ID:1
ncbi_taxonomy
Filobasidiella/Cryptococcus neoformans species complex
NCBITaxon:292817
NCBITaxon:37768
NCBITaxon:37769
NCBITaxon:413065
GC_ID:1
ncbi_taxonomy
Cryptococcus bacillisporus
Cryptococcus neoformans B
Cryptococcus neoformans serotype B
Cryptococcus neoformans serotype C
Cryptococcus neoformans var. gatti
Cryptococcus neoformans var. gattii
Cryptococcus neoformans var. shanghaiensis
Filobasidiella bacillispora
Filobasidiella neoformans var. bacillispora
Filobasidiella neoformans var. gattii
anamorph of Filobasidiella bacillispora
Cryptococcus gattii
GC_ID:11
Streptococcus equi subsp. zooepidemicus str. MGCS10565
Streptococcus equi subsp. zooepidemicus strain MGCS10565
ncbi_taxonomy
Streptococcus equi subsp. zooepidemicus MGCS10565
GC_ID:11
PMID:21602330
Listeria monocytogenes str. HCC23
Listeria monocytogenes strain HCC23
ncbi_taxonomy
Listeria monocytogenes HCC23
GC_ID:1
PMID:23020233
ncbi_taxonomy
Amoebozoa
GC_ID:11
PMID:19047519
Pseudomonas aeruginosa str. LESB58
Pseudomonas aeruginosa strain LESB58
ncbi_taxonomy
Pseudomonas aeruginosa LESB58
GC_ID:1
ncbi_taxonomy
Nucleopolyhedrovirus
Alphabaculovirus
GC_ID:1
ncbi_taxonomy
y
yeast
NCBITaxon:559292
Saccharomyces cerevisiae S288c
y
PRO:DAN
yeast
PRO:DAN
GC_ID:11
Streptococcus pneumoniae str. ATCC 700669
Streptococcus pneumoniae strain ATCC 700669
ncbi_taxonomy
Streptococcus pneumoniae ATCC 700669
NCBITaxon:662101
NCBITaxon:662104
GC_ID:11
PMID:10319482
ncbi_taxonomy
Bacillus coli
Bacterium coli
Bacterium coli commune
Enterococcus coli
Escherchia coli
Eschericia coli
bacterium E3
NCBITaxon:562
Escherichia coli
GC_ID:11
PMID:18952803
Helicobacter pylori str. G27
Helicobacter pylori strain G27
ncbi_taxonomy
Helicobacter pylori G27
GC_ID:11
Listeria monocytogenes str. L99
Listeria monocytogenes strain L99
ncbi_taxonomy
Listeria monocytogenes L99
GC_ID:11
Escherichia coli str. Vir68
Escherichia coli strain Vir68
ncbi_taxonomy
Escherichia coli Vir68
GC_ID:1
ncbi_taxonomy
Trypanosomatidae
GC_ID:1
ncbi_taxonomy
Leishmania (Leishmania) donovani
Leishmania donovani
GC_ID:1
ncbi_taxonomy
Leishmania (Leishmania) major
Leishmania tropica major
NCBITaxon:5664
Leishmania major
GC_ID:1
ncbi_taxonomy
Leishmania (Leishmania) mexicana
Leishmania mexicana
NCBITaxon:5662
GC_ID:1
ncbi_taxonomy
Leishmania (Leishmania) infantum
Leishmania donovani infantum
Leishmania infantum
GC_ID:11
Bacillus anthracis CDC 684
Bacillus anthracis strain CDC 684
ncbi_taxonomy
Bacillus anthracis CDC 684/NRRL 349S/NRS 234
NCBITaxon:568206
Bacillus anthracis str. CDC 684
NCBITaxon:634178
GC_ID:11
Listeria monocytogenes serotype 4b strain CLIP 80459
Listeria monocytogenes str. Clip80459
Listeria monocytogenes strain Clip80459
ncbi_taxonomy
Listeria monocytogenes Clip80459
Listeria monocytogenes Clip81459
Listeria monocytogenes strain CLIP 80459 serovar 4b
Listeria monocytogenes serotype 4b str. CLIP 80459
GC_ID:1
ncbi_taxonomy
Trypanosoma
GC_ID:1
ncbi_taxonomy
Trypanosoma (Trypanozoon) brucei
Trypanosoma brucei subgroup
Trypanosoma brucei
GC_ID:1
ncbi_taxonomy
Trypanosoma cruzi
GC_ID:11
Helicobacter pylori str. P12
Helicobacter pylori strain P12
ncbi_taxonomy
Helicobacter pylori P12
GC_ID:11
PMID:19815525
Escherichia coli O26:H11 11368
Escherichia coli O26:H11 strain 11368
ncbi_taxonomy
Escherichia coli O26:H11 str. 11368
GC_ID:11
PMID:18952797
Escherichia coli O127:H6 E2348/69
Escherichia coli O127:H6 strain E2348/69
ncbi_taxonomy
Escherichia coli 0127:H6 str. E2348/69
Escherichia coli O127:H6 str. E2348/69
GC_ID:1
ncbi_taxonomy
Entamoeba histolytica
GC_ID:11
Vibrio cholerae str. M66-2
Vibrio cholerae strain M66-2
ncbi_taxonomy
Vibrio cholerae M66-2
GC_ID:1
apicomplexans
ncbi_taxonomy
apicomplexans
Apicomplexa
GC_ID:1
ncbi_taxonomy
Cryptosporidium parvum
GC_ID:1
ncbi_taxonomy
Toxoplasma gondii
GC_ID:1
ncbi_taxonomy
Plasmodium
GC_ID:1
ncbi_taxonomy
Plasmodium berghei (strain ANKA)
Plasmodium berghei str. ANKA
Plasmodium berghei strain ANKA
Plasmodium berghei ANKA
ncbi_taxonomy
malaria parasite
NCBITaxon:5833
Plasmodium falciparum
malaria parasite
PRO:DAN
GC_ID:11
Escherichia coli str. IAI1
Escherichia coli strain IAI1
ncbi_taxonomy
Escherichia coli IAI1
GC_ID:11
Escherichia coli str. S88
Escherichia coli strain S88
ncbi_taxonomy
Escherichia coli S88
GC_ID:11
ncbi_taxonomy
Escherichia coli 55989
GC_ID:11
ncbi_taxonomy
NCBITaxon:585056
Escherichia coli UMN026
GC_ID:11
ncbi_taxonomy
NCBITaxon:585057
Escherichia coli IAI39
GC_ID:11
PMID:19815525
Escherichia coli O103:H2 strain 12009
ncbi_taxonomy
Escherichia coli O103:H2 str. 12009
GC_ID:11
PMID:19815525
Escherichia coli O111:H- strain 11128
ncbi_taxonomy
Escherichia coli O111:H- str. 11128
GC_ID:11
Escherichia coli str. ED1a
Escherichia coli strain ED1a
ncbi_taxonomy
Escherichia coli ED1a
GC_ID:1
ncbi_taxonomy
Plasmodium yoelli
Plasmodium yoelii
GC_ID:11
ncbi_taxonomy
Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
GC_ID:11
PMID:10319519
PMID:10939679
PMID:12072558
PMID:15653929
PMID:15653930
PMID:3231714
PMID:9731304
ncbi_taxonomy
Samonella
Salmonella
NCBITaxon:149049
GC_ID:11
PMID:15653929
PMID:15653930
PMID:7149525
ncbi_taxonomy
Salmonella cholerae-suis subsp. cholerae-suis
Salmonella choleraesuis subsp. choleraesuis
Salmonella enterica I
Salmonella enterica subsp. I
Salmonella enterica subsp. enterica
GC_ID:11
PMID:17283804
Bacillus anthracis A0248
Bacillus anthracis strain A0248
ncbi_taxonomy
Bacillus anthracis str. A0248
GC_ID:11
Helicobacter pylori str. B38
Helicobacter pylori strain B38
ncbi_taxonomy
Helicobacter pylori B38
GC_ID:11
Escherichia coli str. BW2952
Escherichia coli strain BW2952
ncbi_taxonomy
Escherichia coli BW2952
GC_ID:1
ncbi_taxonomy
Exophilia dermatitidis
Wangiella dermatitidis
Exophiala dermatitidis
GC_ID:11
PMID:26834722
ncbi_taxonomy
Shigella
GC_ID:11
PMID:16561743
ncbi_taxonomy
Shigella boydii
GC_ID:11
ncbi_taxonomy
Shigella paradysenteriae
NCBITaxon:623
Shigella flexneri
Caenorhabditis elegans
roundworm
GC_ID:1
roundworm
ncbi_taxonomy
Rhabditis elegans
w
worm
NCBITaxon:6239
Caenorhabditis elegans
w
PRO:DAN
worm
PRO:DAN
GC_ID:1
ncbi_taxonomy
SARS coronavirus ExoN1
GC_ID:11
Yersinia
ncbi_taxonomy
Yersinia <bacteria>
GC_ID:11
ncbi_taxonomy
Bacterium enterocoliticum
NCBITaxon:630
Yersinia enterocolitica
GC_ID:11
PMID:15084509
ncbi_taxonomy
Bacillus pestis
Bacterium pestis
Pasteurella pestis
Pestisella pestis
Yersinia pseudotuberculosis subsp. pestis
Ypes-
NCBITaxon:632
Yersinia pestis
Ypes-
PRO:DAN
NCBITaxon:1161941
GC_ID:11
PMID:2223608
PMID:23919959
ncbi_taxonomy
Bacillus pseudotuberkulosis
Bacterium pseudotuberculosis
Pasteurella lymphangitidis
Pasteurella pseudotuberculosis
Shigella pseudotuberculosis
[Pasteurella] lymphangitidis
Yersinia pseudotuberculosis
NCBITaxon:1471792
NCBITaxon:1471793
GC_ID:11
PMID:27539016
ncbi_taxonomy
Edwardsiella anguillimortifera
Paracolobactrum anguillimortiferum
Edwardsiella tarda
GC_ID:11
Listeria monocytogenes str. 08-5923
Listeria monocytogenes strain 08-5923
ncbi_taxonomy
Listeria monocytogenes 08-5923
GC_ID:11
PMID:11155981
PMID:12067377
PMID:12807216
PMID:1380286
PMID:1380289
PMID:15388703
PMID:16560691
PMID:17012583
PMID:17158971
PMID:19567585
PMID:7520733
PMID:8347521
PMID:8934910
ncbi_taxonomy
Aeromonas
NCBITaxon:1471787
NCBITaxon:1471788
NCBITaxon:582196
NCBITaxon:582198
NCBITaxon:582214
NCBITaxon:582215
NCBITaxon:582216
NCBITaxon:582217
NCBITaxon:582218
NCBITaxon:582219
NCBITaxon:582220
NCBITaxon:582221
NCBITaxon:582222
NCBITaxon:582223
NCBITaxon:582224
NCBITaxon:582225
NCBITaxon:582226
NCBITaxon:582228
NCBITaxon:582229
NCBITaxon:582231
NCBITaxon:582236
NCBITaxon:582237
NCBITaxon:582240
NCBITaxon:582250
NCBITaxon:582251
NCBITaxon:582253
NCBITaxon:582254
NCBITaxon:582265
NCBITaxon:582266
NCBITaxon:582267
NCBITaxon:582279
NCBITaxon:582282
NCBITaxon:582284
NCBITaxon:582286
NCBITaxon:582287
NCBITaxon:582289
NCBITaxon:582290
NCBITaxon:582291
NCBITaxon:582292
NCBITaxon:582295
NCBITaxon:582297
NCBITaxon:582299
NCBITaxon:582300
NCBITaxon:582302
NCBITaxon:582303
NCBITaxon:582304
NCBITaxon:582305
NCBITaxon:582306
NCBITaxon:582307
NCBITaxon:582308
NCBITaxon:582309
NCBITaxon:582310
NCBITaxon:582311
NCBITaxon:582312
NCBITaxon:582313
NCBITaxon:582314
NCBITaxon:582315
NCBITaxon:582316
NCBITaxon:582317
NCBITaxon:582318
NCBITaxon:582319
NCBITaxon:582320
NCBITaxon:582321
NCBITaxon:582322
NCBITaxon:582323
NCBITaxon:582324
NCBITaxon:98358
GC_ID:11
PMID:16560691
PMID:19965992
PMID:23485124
PMID:932684
ncbi_taxonomy
Aeromonas dourgesi
Aeromonas hydrophilia
Aeromonas liquefaciens
Bacillus hydrophilus
Bacillus hydrophilus fuscus
Bacterium hydrophilum
Proteus hydrophilus
Proteus ichthyosmius
Pseudomonas hydrophila
Aeromonas hydrophila
NCBITaxon:697046
GC_ID:11
PMID:19965992
ncbi_taxonomy
Bacillus salmonicida
Bacterium salmonicida
Proteus salmonicida
Aeromonas salmonicida
GC_ID:11
Listeria monocytogenes str. 08-5578
Listeria monocytogenes strain 08-5578
ncbi_taxonomy
Listeria monocytogenes 08-5578
GC_ID:11
Neisseria meningitidis str. alpha14
Neisseria meningitidis strain alpha14
ncbi_taxonomy
Neisseria meningitidis alpha14
GC_ID:11
PMID:9272984
ncbi_taxonomy
Bacillo virgola del Koch
Bacillus cholerae
Bacillus cholerae-asiaticae
Kommabacillus
Liquidivibrio cholerae
Microspira comma
Pacinia cholerae-asiaticae
Spirillum cholerae
Spirillum cholerae-asiaticae
Vibrio choleae
Vibrio cholera
Vibrio cholerae-asiaticae
Vibrio comma
Vibrio cholerae
GC_ID:11
ncbi_taxonomy
Legionella pneumophila serogroup 1
NCBITaxon:665030
GC_ID:11
Staphylococcus aureus subsp. aureus str. ED98
Staphylococcus aureus subsp. aureus strain ED98
ncbi_taxonomy
Staphylococcus aureus ED98
Staphylococcus aureus subsp. aureus ED98
GC_ID:1
ncbi_taxonomy
Murine cytomegalovirus (strain K181)
GC_ID:1
ncbi_taxonomy
Coronavirinae
GC_ID:1
ncbi_taxonomy
Alphacoronavirus-1
Alphacoronavirus 1
SARSr-CoV
GC_ID:1
ncbi_taxonomy
SARS-like coronavirus
SARS-related coronavirus
Severe acute respiratory syndrome-related coronavirus
GC_ID:1
ncbi_taxonomy
Human metapneumovirus CAN97-83
GC_ID:1
ncbi_taxonomy
Mileewa branchiuma
GC_ID:11
ncbi_taxonomy
Staphylococcus aureus 04-02981
GC_ID:1
domestic silkworm
silk moth
silkworm
ncbi_taxonomy
Bombyx mori
GC_ID:4
PMID:12949158
Mycoplasma gallisepticum R(low)
Mycoplasma gallisepticum strain R(low)
ncbi_taxonomy
Mycoplasma gallisepticum str. R(low)
GC_ID:11
PMID:10843050
PMID:15280320
PMID:15388716
PMID:17220461
PMID:2223605
PMID:29923825
ncbi_taxonomy
Pasteurellaceae Pohl 1981
Pasteurellaceae
NCBITaxon:185836
GC_ID:1
greater wax moth
ncbi_taxonomy
Galleria mellonela
Galleria melonella
Galleria mellonella
GC_ID:11
Haemophilus influenzae KW20
Haemophilus influenzae Rd
ncbi_taxonomy
NCBITaxon:71421
Haemophilus influenzae Rd KW20
GC_ID:11
PMID:1847295
ncbi_taxonomy
Actinobacillus pleuropneumonia
Haemophilus pleuropneumoniae
Actinobacillus pleuropneumoniae
saccharomyceta
GC_ID:1
ncbi_taxonomy
saccharomyceta
Drosophila melanogaster
fruit fly
GC_ID:1
fruit fly
ncbi_taxonomy
Drosophila melangaster
Sophophora melanogaster
NCBITaxon:7227
Drosophila melanogaster
fruit fly
GC_ID:11
ncbi_taxonomy
Bacterium influenzae
Coccobacillus pfeifferi
Haemophilus meningitidis
Influenza-bacillus
Mycobacterium influenzae
Haemophilus influenzae
GC_ID:1
ncbi_taxonomy
NCBITaxon:73239
Plasmodium yoelii yoelii
GC_ID:11
PMID:15184562
ncbi_taxonomy
Bacterium multocidum
Micrococcus gallicidus
Pasteurella cholerae-gallinarum
Pasteurella gallicida
Pateurella multocida
Pasteurella multocida
NCBITaxon:746
GC_ID:11
PMID:10028248
PMID:8782683
ncbi_taxonomy
Pasteurella haemolytica
Mannheimia haemolytica
GC_ID:1
ncbi_taxonomy
Nidovirales
NCBITaxon:802
GC_ID:11
PMID:10425758
PMID:11837299
PMID:12508871
PMID:7857789
PMID:8240958
PMID:8863415
ncbi_taxonomy
"Bartonia" Strong et al. 1913
"Grahamella" Brumpt 1911
"Grahmia" Tartakowsky 1910
"Rocha-Limae" (sic) Machiavello 1947
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
Grahamella (ex Brumpt 1911) Ristic and Kreier 1984
Grahmia
Rocha-Limae
Rochalimaea
Rochalimaea (Macchiavello 1947) Krieg 1961
Bartonella
Vertebrata <Metazoa>
Vertebrata
vertebrates
GC_ID:1
Vertebrata
vertebrates
ncbi_taxonomy
vertebrates
Vertebrata <Metazoa>
GC_ID:11
PMID:9226923
ncbi_taxonomy
Coxiella burnetii8
Rickettsia burneti
Rickettsia diaporica
Coxiella burnetii
GC_ID:11
PMID:10939649
PMID:11491333
PMID:14662925
PMID:9103608
ncbi_taxonomy
Rickettsia
Danio rerio
leopard danio
zebra danio
zebra fish
zebrafish
NCBITaxon:27702
NCBITaxon:37966
GC_ID:1
leopard danio
zebra danio
zebra fish
zebrafish
ncbi_taxonomy
Brachidanio rerio
Brachydanio rerio
Brachydanio rerio frankei
Cyprinus rerio
Danio frankei
Danio rerio frankei
NCBITaxon:7955
Danio rerio
zebrafish
GC_ID:1
ncbi_taxonomy
Lythrurus
GC_ID:1
ncbi_taxonomy
Bovine herpesvirus type 1.1
GC_ID:1
PMID:15062801
salmonids
ncbi_taxonomy
Salmonidae
NCBITaxon:1311475
GC_ID:1
rainbow trout
ncbi_taxonomy
Onchorhynchus mykiss
Oncorhynchus nerka mykiss
Parasalmo mykiss
Salmo mykiss
Oncorhynchus mykiss
GC_ID:1
ncbi_taxonomy
Melanogaster
GC_ID:11
PMID:16403855
ncbi_taxonomy
'Burkholderiales'
Burkholderia/Oxalobacter/Ralstonia group
Burkholderiales
NCBITaxon:83553
GC_ID:11
PMID:10319462
PMID:11211265
PMID:21048221
PMID:21048222
PMID:23620152
PMID:25618261
PMID:9103632
PMID:9103637
ncbi_taxonomy
Bedsonia
Chlamydophila
Miyagawanella
Rakeia
Rickettsiaformis
Chlamydia
GC_ID:11
PMID:10192388
PMID:10319462
PMID:8102247
PMID:8347519
ncbi_taxonomy
Chlamydozoon trachomatis
Rickettsia trachomae
Rickettsia trachomatis
Chlamydia trachomatis
GC_ID:11
PMID:12218036
ncbi_taxonomy
Mycobacterium tuberculosis CSU#93
Mycobacterium tuberculosis CDC1551
GC_ID:11
PMID:12218036
PMID:12368430
PMID:9634230
Mycobacterium tuberculosis str. H37Rv
Mycobacterium tuberculosis strain H37Rv
ncbi_taxonomy
NCBITaxon:83332
Mycobacterium tuberculosis H37Rv
GC_ID:11
Escherichia coli K12
ncbi_taxonomy
Ec-
NCBITaxon:83333
Escherichia coli K-12
Ec-
PRO:DAN
GC_ID:11
ncbi_taxonomy
Escherichia coli 0157:H7
Escherichia coli O157:H7
NCBITaxon:811
GC_ID:11
PMID:10319462
PMID:8102247
PMID:8347519
ncbi_taxonomy
Chlamydophila pneumoniae
Chlamydia pneumoniae
NCBITaxon:1761
GC_ID:11
PMID:11837321
PMID:1736962
PMID:19244447
ncbi_taxonomy
Corynebacterineae
Corynebacteriales
Corynebacterineae
GC_ID:1
ncbi_taxonomy
charr
Salvelinus alpinus alpinus
GC_ID:1
ncbi_taxonomy
Porcine circovirus Type II
Porcine circovirus type 2
Porcine circovirus 2
GC_ID:11
PMID:9252185
Helicobacter pylori (strain 26695)
Helicobacter pylori str. 26695
Helicobacter pylori strain 26695
ncbi_taxonomy
Helicobacter pylori ATCC 700392
Helicobacter pylori KE26695
NCBITaxon:85962
Helicobacter pylori 26695
GC_ID:11
PMID:9923682
Helicobacter pylori str. J99
Helicobacter pylori strain J99
ncbi_taxonomy
NCBITaxon:85963
Helicobacter pylori J99
GC_ID:11
Legionella pneumophila str. 130b
Legionella pneumophila strain 130b
ncbi_taxonomy
Legionella pneumophila ATCC BAA-74
Legionella pneumophila serogroup 1 strain 130b
Legionella pneumophila 130b
NCBITaxon:9099
GC_ID:1
turkeys
ncbi_taxonomy
Phasianidae
Gallus gallus
bantam
chicken
chickens
GC_ID:1
bantam
chicken
chickens
ncbi_taxonomy
Gallus domesticus
Gallus gallus domesticus
chick-
chicken
NCBITaxon:9031
Gallus gallus
chick-
PRO:DAN
chicken
NCBITaxon:41530
NCBITaxon:601
NCBITaxon:72667
GC_ID:11
PMID:10319519
PMID:10758910
PMID:15653930
PMID:16558776
PMID:9336938
ncbi_taxonomy
Bacillus typhi
Bacterium (subgen. Eberthella) typhi
Salmonella choleraesuis serovar Typhi
Salmonella choleraesuis typhi
Salmonella enterica ser. typhi
Salmonella enterica serotype Typhi
Salmonella enterica serovar Typhi
Salmonella typhi
NCBITaxon:90370
Salmonella enterica subsp. enterica serovar Typhi
NCBITaxon:41532
NCBITaxon:59210
NCBITaxon:602
GC_ID:11
PMID:10758910
PMID:15653930
PMID:9336938
ncbi_taxonomy
Bacillus typhimurium
Salmonella choleraesuis serotype typhimurium
Salmonella enterica 1,4,[5],12,:i:1,2
Salmonella enterica ser. typhimurium
Salmonella enterica serotype Typhimurium
Salmonella enterica serovar Typhimurium
Salmonella enterica subsp. enterica serovar 1,4,[5],12,:i:1,2
Salmonella typhi-murium
Salmonella typhimurium
Samonella typhimurium
Styphi-
NCBITaxon:90371
Salmonella enterica subsp. enterica serovar Typhimurium
Styphi-
PRO:DAN
GC_ID:11
PMID:21478351
Salmonella enterica subsp. enterica serovar Typhimurium strain ST4/74
ncbi_taxonomy
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
GC_ID:11
PMID:20212322
ncbi_taxonomy
Bacillus/Lactobacillus/Streptococcus group
Firmibacteria
Bacilli
GC_ID:11
PMID:27620848
ncbi_taxonomy
Enterobacteriaceae and related endosymbionts
Enterobacteriaceae group
Enterobacteriales
enterobacteria
gamma-3 proteobacteria
Enterobacterales
GC_ID:1
whales, hippos, ruminants, pigs, camels etc.
ncbi_taxonomy
even-toed ungulates
Cetartiodactyla
GC_ID:11
Staphylococcus aureus subsp. aureus str. NCTC 8325
Staphylococcus aureus subsp. aureus strain NCTC 8325
ncbi_taxonomy
Staphylococcus aureus NCTC 8325
NCBITaxon:93061
Staphylococcus aureus subsp. aureus NCTC 8325
NCBITaxon:95751
GC_ID:1
ncbi_taxonomy
influenza A virus (A/goose/Guangdong/1/96/(H5N1))
NCBITaxon:93838
Influenza A virus (A/Goose/Guangdong/1/96(H5N1))
Influenza A virus (A/goose/Guangdong/1/1996(H5N1))
GC_ID:1
New World monkeys
monkey
monkeys
ncbi_taxonomy
Platyrrhini
GC_ID:1
ncbi_taxonomy
Catarrhini
GC_ID:1
Old World monkeys
monkey
monkeys
ncbi_taxonomy
Cercopithecidae
green monkey
ncbi_taxonomy
GrMonkey-
NCBITaxon:9534
Chlorocebus aethiops
Chlorocebus aethiops
绿猴属
green monkey
GrMonkey-
PRO:DAN
Homo sapiens
human
human being
man
GC_ID:1
human
man
ncbi_taxonomy
Home sapiens
Homo sampiens
Homo sapeins
Homo sapian
Homo sapians
Homo sapien
Homo sapience
Homo sapiense
Homo sapients
Homo sapines
Homo spaiens
Homo spiens
Humo sapiens
h
human
NCBITaxon:9606
Homo sapiens
Homo sapiens
人类
h
PRO:DAN
human
PRO:DAN
NCBITaxon:77150
GC_ID:1
black ferret
domestic ferret
ferret
ncbi_taxonomy
Mustela furo
Mustela putoris furo
Mustela putorius furo
GC_ID:1
pig
pigs
swine
wild boar
ncbi_taxonomy
Sus scrofus
pig
pig-
NCBITaxon:9823
Sus scrofa
pig
pig-
PRO:DAN
GC_ID:1
ncbi_taxonomy
Bovidae
NCBITaxon:272461
GC_ID:1
bovine
cattle
cow
dairy cow
domestic cattle
domestic cow
ncbi_taxonomy
Bos Tauurus
Bos bovis
Bos primigenius taurus
cow
cow-
NCBITaxon:9913
Bos taurus
cow
cow-
PRO:DAN
NCBITaxon:57076
GC_ID:1
domestic goat
goat
goats
ncbi_taxonomy
Capra aegagrus hircus
Carpa hircus
South African angora goat
Capra hircus
NCBITaxon:870965
GC_ID:11
PMID:11677609
Salmonella enterica subsp. enterica serovar Typhimurium LT2
Salmonella enterica subsp. enterica serovar Typhimurium strain LT2
Salmonella enterica subsp. enterica serovar Typhimurium strain LT2-LTL2
ncbi_taxonomy
Salmonella typhimurium LT2
SaltyLT2-
NCBITaxon:99287
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
SaltyLT2-
PRO:DAN
NCBITaxon:9936
GC_ID:1
domestic sheep
lambs
sheep
wild sheep
ncbi_taxonomy
Ovis ammon aries
Ovis orientalis aries
Ovis ovis
NCBITaxon:9940
Ovis aries
sheep
GC_ID:1
ncbi_taxonomy
Caprinae
NCBITaxon:34833
NCBITaxon:9985
GC_ID:1
European rabbit
Japanese white rabbit
domestic rabbit
rabbit
rabbits
ncbi_taxonomy
Lepus cuniculus
rabbit-
NCBITaxon:9986
Oryctolagus cuniculus
rabbit
rabbit-
PRO:DAN
Rodentia
rodent
GC_ID:1
rodent
ncbi_taxonomy
rodents
NCBITaxon:9989
Rodentia
rodent
planned process
planned process
Injecting mice with a vaccine in order to test its efficacy
A processual entity that realizes a plan which is the concretization of a plan specification.
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some
objectives is a planned process.
Bjoern Peters
branch derived
6/11/9: Edited at workshop. Used to include: is initiated by an agent
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
planned process
regulator role
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
regulator
OBI
regulator role
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
regulatory role
material supplier role
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 provider role
supplier
material supplier role
classified data set
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.
PERSON: James Malone
PERSON: Monnie McGee
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.
PERSON: Alan Ruttenberg
processed material
culture medium
A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178
Modification made by JZ.
Person: Jennifer Fostel, Jie Zheng
OBI
culture medium
material processing
A cell lysis, production of a cloning vector, creating a buffer.
A planned process which results in physical changes in a specified input material
PERSON: Bjoern Peters
PERSON: Frank Gibson
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
PERSON: Philippe Rocca Serra
material transformation
OBI branch derived
material processing
specimen role
liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
blood taken from animal: animal continues in study, whereas blood has role specimen.
something taken from study subject, leaves the study and becomes the specimen.
parasite example
- when parasite in people we study people, people are subjects and parasites are specimen
- when parasite extracted, they become subject in the following study
specimen can later be subject.
GROUP: Role Branch
OBI
specimen role
antigen 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
OBI
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.
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Philippe Rocca-Serra
PERSON: Susanna Sansone
GROUP: OBI
organization
organization
组织
regulatory agency
The US Environmental Protection 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.
GROUP: OBI Biomaterial Branch
WEB: en.wikipedia.org/wiki/Regulator
regulatory agency
material transformation objective
The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
an objective specifiction that creates an specific output object from input materials.
PERSON: Bjoern Peters
PERSON: Frank Gibson
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
PERSON: Philippe Rocca-Serra
artifact creation objective
GROUP: OBI PlanAndPlannedProcess Branch
material transformation objective
manufacturing
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.
PERSON: Bjoern Peters
PERSON: Frank Gibson
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
PERSON: Philippe Rocca-Serra
GROUP: OBI PlanAndPlannedProcess Branch
manufacturing
manufacturing objective
is the objective to manufacture a material of a certain function (device)
PERSON: Bjoern Peters
PERSON: Frank Gibson
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
PERSON: Philippe Rocca-Serra
GROUP: OBI PlanAndPlannedProcess Branch
manufacturing objective
manufacturer role
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.
GROUP: Role Branch
OBI
manufacturer role
material separation objective
The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
is an objective to transform a material entity into spatially separated components.
PPPB branch
PPPB branch
material separation objective
clustered data set
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.
PERSON: James Malone
PERSON: Monnie McGee
data set with assigned discovered class labels
AR thinks could be a data item instead
clustered data set
specimen collection process
drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
A planned process with the objective of collecting a specimen.
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
Philly2013: The specimen_role for the specimen is created during the specimen collection process.
label changed to 'specimen collection process' on 10/27/2014, details see tracker:
http://sourceforge.net/p/obi/obi-terms/716/
Bjoern Peters
specimen collection
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
6/9/09: used at workshop
specimen collection process
class prediction data transformation
A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction.
James Malone
supervised classification data transformation
PERSON: James Malone
class prediction data transformation
portioning objective
The objective to obtain multiple aliquots of an enzyme preparation.
A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
portioning objective
separation into different composition objective
The objective to obtain cells contained in a sample of blood.
A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities).
We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
separation into different composition objective
specimen collection objective
The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
A objective specification to obtain a material entity for potential use as an input during an investigation.
Bjoern Peters
Bjoern Peters
specimen collection objective
support vector machine
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.
James Malone
Ryan Brinkman
SVM
PERSON: Ryan Brinkman
support vector machine
decision tree induction objective
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.
James Malone
decision tree induction objective
decision tree building data transformation
A decision tree building data transformation is a data transformation that has objective decision tree induction.
James Malone
PERSON: James Malone
decision tree building data transformation
GenePattern software
a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks.
James Malone
Person:Helen Parkinson
WEB: http://www.broadinstitute.org/cancer/software/genepattern/
GenePattern software
host role
In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09
host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role
30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition
GROUP: Role Branch
30 Mar09 submitted by vaccine community
OBI
http://en.wikipedia.org/wiki/Host_(biology)
host role
peak matching
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
James Malone
Ryan Brinkman
PERSON: Ryan Brinkman
peak matching
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
k-NN
PERSON: James Malone
k-nearest neighbors
CART
A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure.
James Malone
classification and regression trees
BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining.
CART
statistical model validation
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.
Helen Parkinson
http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29
statistical model validation
material maintenance objective
An objective specification maintains some or all of the qualities of a material over time.
PERSON: Bjoern Peters
PERSON: Bjoern Peters
material maintenance objective
manufacturer
A person or organization that has a manufacturer role
manufacturer
material maintenance
a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
material maintenance
service provider role
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
PERSON:Helen Parkinson
service provider role
processed specimen
A tissue sample that has been sliced and stained for a histology study.
A blood specimen that has been centrifuged to obtain the white blood cells.
A specimen that has been intentionally physically modified.
Bjoern Peters
Bjoern Peters
A tissue sample that has been sliced and stained for a histology study.
processed specimen
categorical label
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.
Bjoern Peters
Bjoern Peters
categorical label
questionnaire
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
questionnaire
specimen from organism
A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
PERSON: Chris Stoeckert, Jie Zheng
tissue specimen
MO_954 organism_part
specimen from organism
secondary cultured cell
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.
Person: Matthew Brush
PERSON: Matthew Brush
A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture.
secondary cultured cell
establishing cell line
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.
Person: Matthew Brush
PERSON:Matthew Brush
establishing cell line
establishing cell line
建立细胞系
secondary cultured cell population
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.
PERSON:Matthew Brush
secondary cell culture sample
PERSON:Matthew Brush
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.
secondary cultured cell population
cell freezing medium
A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles.
PERSON: Matthew Brush
cell freezing medium
categorical value specification
A value specification that is specifies one category out of a fixed number of nominal categories
PERSON:Bjoern Peters
categorical value specification
value specification
The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
PERSON:Bjoern Peters
value specification
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
OBIB, OBI
Biobank
collection of specimens
histologic grade according to AJCC 7th edition
G4: Undifferentiated
G1:Well differentiated
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.
Chris Stoeckert, Helena Ellis
NCI BBRB, OBI
NCI BBRB
histologic grade according to AJCC 7th edition
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.
Chris Stoeckert, Helena Ellis
Histologic Grade (Fuhrman Nuclear Grading System)
NCI BBRB, OBI
NCI BBRB
histologic grade according to the Fuhrman Nuclear Grading System
histologic grade for ovarian tumor
A categorical value specification that is a histologic grade assigned to a ovarian tumor.
Chris Stoeckert, Helena Ellis
NCI BBRB, OBI
NCI BBRB
histologic grade for 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.
Chris Stoeckert, Helena Ellis
NCI BBRB, OBI
NCI BBRB
histologic grade for ovarian tumor according to a two-tier grading system
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).
Chris Stoeckert, Helena Ellis
NCI BBRB, OBI
NCI BBRB
histologic grade for ovarian tumor according to the World Health Organization
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.
Chris Stoeckert, Helena Ellis
pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition)
NCI BBRB, OBI
NCI BBRB
pathologic primary tumor stage for colon and rectum according to 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.
Chris Stoeckert, Helena Ellis
pT: Pathologic spread lung primary tumor (AJCC 7th Edition)
NCI BBRB, OBI
NCI BBRB
pathologic primary tumor stage for lung according to 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.
Chris Stoeckert, Helena Ellis
pT: Pathologic spread kidney primary tumor (AJCC 7th Edition)
NCI BBRB, OBI
NCI BBRB
pathologic primary tumor stage for kidney according to 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.
Chris Stoeckert, Helena Ellis
pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition)
NCI BBRB, OBI
NCI BBRB
pathologic primary tumor stage for ovary according to 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.
Chris Stoeckert, Helena Ellis
pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)
NCI BBRB, OBI
NCI BBRB
pathologic lymph node stage for colon and rectum according to 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.
Chris Stoeckert, Helena Ellis
pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)
NCI BBRB, OBI
NCI BBRB
pathologic lymph node stage for lung according to AJCC 7th edition
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.
Chris Stoeckert, Helena Ellis
pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition)
NCI BBRB, OBI
NCI BBRB
pathologic lymph node stage for kidney according to 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.
Chris Stoeckert, Helena Ellis
pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition)
NCI BBRB, OBI
NCI BBRB
pathologic lymph node stage for ovary according to 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.
Chris Stoeckert, Helena Ellis
M: colon distant metastases (AJCC 7th Edition)
NCI BBRB, OBI
NCI BBRB
pathologic distant metastases stage for colon according to 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.
Chris Stoeckert, Helena Ellis
M: lung distant metastases (AJCC 7th Edition)
NCI BBRB, OBI
NCI BBRB
pathologic distant metastases stage for lung according to 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.
Chris Stoeckert, Helena Ellis
M: kidney distant Metastases (AJCC 7th Edition)
NCI BBRB, OBI
NCI BBRB
pathologic distant metastases stage for kidney according to 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.
Chris Stoeckert, Helena Ellis
M: ovarian distant metastases (AJCC 7th Edition)
NCI BBRB, OBI
NCI BBRB
pathologic distant metastases stage for ovary according to 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.
Chris Stoeckert, Helena Ellis
Clinical tumor stage group (AJCC 7th Edition)
NCI BBRB, OBI
NCI BBRB
clinical tumor stage group according to 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.
Chris Stoeckert, Helena Ellis
Clinical FIGO stage
NCI BBRB, OBI
NCI BBRB
International Federation of Gynecology and Obstetrics cervical cancer stage value specification
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.
Chris Stoeckert, Helena Ellis
Pathologic Tumor Stage Grouping for ovarian cancer (FIGO)
NCI BBRB, OBI
NCI BBRB
International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
performance status value specification
A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life).
Chris Stoeckert, Helena Ellis
Performance Status Scale
https://en.wikipedia.org/wiki/Performance_status
NCI BBRB
performance status value specification
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.
Chris Stoeckert, Helena Ellis
ECOG score
NCI BBRB, OBI
NCI BBRB
Eastern Cooperative Oncology Group score value specification
Karnofsky score vaue specification
A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment.
Chris Stoeckert, Helena Ellis
Karnofsky Score
NCI BBRB, OBI
NCI BBRB
Karnofsky score vaue specification
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
PERSON: Susanna Sansone
GROUP: OBI Biomaterial Branch
Epstein Barr virus transformed B cell
organism
animal
fungus
plant
virus
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
13-02-2009:
OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus.
This issue is outside the scope of OBI.
GROUP: OBI Biomaterial Branch
WEB: http://en.wikipedia.org/wiki/Organism
obi
OBI:0100026
organism
organism
specimen
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
A material entity that has the specimen role.
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
PERSON: James Malone
PERSON: Philippe Rocca-Serra
GROUP: OBI Biomaterial Branch
specimen
cultured cell population
A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948).
A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293).
A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line.
PERSON:Matthew Brush
cell culture sample
PERSON:Matthew Brush
The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.
cultured cell population
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
James Malone
Melanie Courtot
Philippe Rocca-Serra
Richard Scheuermann
Ryan Brinkman
Tina Hernandez-Boussard
data analysis
data processing
Branch editors
data transformation
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
Person:Helen Parkinson
leave one out cross validation method
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).
Elisabetta Manduchi
James Malone
Philippe Rocca-Serra
WEB: http://en.wikipedia.org/wiki/K-means
k-means clustering
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).
James Malone
WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_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.
Elisabetta Manduchi
James Malone
Melanie Courtot
Philippe Rocca-Serra
data projection
PERSON: Elisabetta Manduchi
PERSON: James Malone
PERSON: Melanie Courtot
dimensionality reduction
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.
Elisabetta Manduchi
James Malone
Melanie Courtot
Philippe Rocca-Serra
pca data reduction
PERSON: Elisabetta Manduchi
PERSON: James Malone
PERSON: Melanie Courtot
principal components analysis dimensionality reduction
data visualization
Generation of a heatmap from a microarray dataset
An planned process that creates images, diagrams or animations from the input data.
Elisabetta Manduchi
James Malone
Melanie Courtot
Tina Boussard
data encoding as image
visualization
PERSON: Elisabetta Manduchi
PERSON: James Malone
PERSON: Melanie Courtot
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
James Malone
PERSON: James Malone
data transformation objective
partitioning data transformation
A partitioning data transformation is a data transformation that has objective partitioning.
James Malone
PERSON: James Malone
partitioning data transformation
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.
Elisabetta Manduchi
James Malone
PERSON: Elisabetta Manduchi
partitioning objective
class discovery data transformation
A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery.
James Malone
clustering data transformation
unsupervised classification data transformation
PERSON: James Malone
class discovery 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.
James Malone
clustering objective
discriminant analysis objective
unsupervised classification objective
PERSON: Elisabetta Manduchi
PERSON: James Malone
class discovery 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.
James Malone
classification objective
supervised classification objective
PERSON: Elisabetta Manduchi
PERSON: James Malone
class prediction 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.
James Malone
rotation estimation objective
WEB: http://en.wikipedia.org/wiki/Cross_validation
cross validation objective
clustered data visualization
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.
James Malone
clustered data visualization
material component separation
Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
a material processing in which components of an input material become segregated in space
Bjoern Peters
IEDB
material component separation
maintaining cell culture
When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture
a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
PlanAndPlannedProcess Branch
OBI branch derived
maintaining cell culture
'establishing cell culture'
a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line).
PERSON:Matthew Brush
PERSON:Matthew Brush
A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms.
establishing cell culture
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
PlanAndPlannedProcess Branch
cell culture passaging
OBI branch derived
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.
cell culture splitting
A genome is a material entity that represents the entirety of an organism's hereditary information. The genome includes both the genes and the non-coding sequences of the DNA and RNA.
Oliver He
Book: Eugene Nester, Denise Anderson, C. Evans Roberts, Jr., Microbiology (Companion Site): A Human Perspective, 7th Edition. Mcgraw Hill, October 18, 2011. ISBN-13: 978-0073375311
WEB: http://en.wikipedia.org/wiki/Genome
genome
A gene is a material entity that represents the entire DNA sequence required for synthesis of a functional protein or RNA molecule.
Oliver He
WEB: http://www.ncbi.nlm.nih.gov/books/NBK21640/
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.
Yongqun He, Bin Zhao
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. .
Yongqun He, Bin Zhao
WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
protein-coding gene type
a gene type that is tRNA, i.e., this gene encodes for a RNA.
Yongqun He, Bin Zhao
WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
RNA gene type
a RNA gene type that is tRNA, i.e., this gene encodes for a rRNA.
Yongqun He, Bin Zhao
WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
rRNA gene type
a RNA gene type that is tRNA, i.e., this gene encodes for a rRNA.
Yongqun He, Bin Zhao
WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
snRNA gene type
a RNA gene type that is tRNA, i.e., this gene encodes for a tRNA.
Yongqun He, Bin Zhao
WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
tRNA gene type
a RNA gene type that is scRNA, i.e., this gene encodes for a scRNA.
Yongqun He, Bin Zhao
WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
scRNA gene type
a RNA gene type that is snoRNA, i.e., this gene encodes for a snoRNA.
Yongqun He, Bin Zhao
WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
snoRNA gene type
a RNA gene type that is miscRNA, i.e., this gene encodes for a miscRNA.
Yongqun He, Bin Zhao
WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
miscRNA gene type
a RNA gene type that is ncRNA, i.e., this gene encodes for a ncRNA.
Yongqun He, Bin Zhao
WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
ncRNA gene type
a gene type that is pseudo, i.e., the gene is a pseudogene.
Yongqun He, Bin Zhao
WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
pseudo gene type
a gene type that is transposon, i.e., the gene encodes for a transposon.
Yongqun He, Bin Zhao
WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
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.
Yongqun He, Bin Zhao
WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
other gene type
a gene type that is "unknown", i.e., the gene product is unknown.
Yongqun He, Bin Zhao
WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
unknown gene type
The genome of an organism of Bacteria
Bin Zhao, Oliver He
2
genome of Bacteria
The genome of an organism of Spirochaetales
Bin Zhao, Oliver He
136
genome of Spirochaetales
The genome of an organism of Borrelia burgdorferi
Bin Zhao, Oliver He
139
genome of Borrelia burgdorferi
The genome of an organism of Campylobacter jejuni
Bin Zhao, Oliver He
197
genome of Campylobacter jejuni
The genome of an organism of Helicobacter pylori
Bin Zhao, Oliver He
210
genome of Helicobacter pylori
The genome of an organism of Brucella
Bin Zhao, Oliver He
234
genome of Brucella
The genome of an organism of Brucella abortus
Bin Zhao, Oliver He
235
genome of Brucella abortus
The genome of an organism of Francisella tularensis
Bin Zhao, Oliver He
263
genome of Francisella tularensis
The genome of an organism of Pseudomonas aeruginosa
Bin Zhao, Oliver He
287
genome of Pseudomonas aeruginosa
The genome of an organism of Rhizobiales
Bin Zhao, Oliver He
356
genome of Rhizobiales
The genome of an organism of Legionella pneumophila
Bin Zhao, Oliver He
446
genome of Legionella pneumophila
The genome of an organism of Neisseria meningitidis
Bin Zhao, Oliver He
487
genome of Neisseria meningitidis
The genome of an organism of Bordetella
Bin Zhao, Oliver He
517
genome of Bordetella
The genome of an organism of Bordetella pertussis
Bin Zhao, Oliver He
520
genome of Bordetella pertussis
The genome of an organism of Enterobacteriaceae
Bin Zhao, Oliver He
543
genome of Enterobacteriaceae
The genome of an organism of Escherichia coli
Bin Zhao, Oliver He
562
genome of Escherichia coli
The genome of an organism of Shigella
Bin Zhao, Oliver He
620
genome of Shigella
The genome of an organism of Shigella boydii
Bin Zhao, Oliver He
621
genome of Shigella boydii
The genome of an organism of Shigella flexneri
Bin Zhao, Oliver He
623
genome of Shigella flexneri
The genome of an organism of Yersinia <bacteria>
Bin Zhao, Oliver He
629
genome of Yersinia <bacteria>
The genome of an organism of Yersinia enterocolitica
Bin Zhao, Oliver He
630
genome of Yersinia enterocolitica
The genome of an organism of Yersinia pestis
Bin Zhao, Oliver He
632
genome of Yersinia pestis
The genome of an organism of Yersinia pseudotuberculosis
Bin Zhao, Oliver He
633
genome of Yersinia pseudotuberculosis
The genome of an organism of Vibrio cholerae
Bin Zhao, Oliver He
666
genome of Vibrio cholerae
The genome of an organism of Pasteurellaceae
Bin Zhao, Oliver He
712
genome of Pasteurellaceae
The genome of an organism of Actinobacillus pleuropneumoniae
Bin Zhao, Oliver He
715
genome of Actinobacillus pleuropneumoniae
The genome of an organism of Haemophilus influenzae
Bin Zhao, Oliver He
727
genome of Haemophilus influenzae
The genome of an organism of Pasteurella multocida
Bin Zhao, Oliver He
747
genome of Pasteurella multocida
The genome of an organism of Bartonella
Bin Zhao, Oliver He
773
genome of Bartonella
The genome of an organism of Chlamydia
Bin Zhao, Oliver He
810
genome of Chlamydia
The genome of an organism of Proteobacteria
Bin Zhao, Oliver He
1224
genome of Proteobacteria
The genome of an organism of Gammaproteobacteria
Bin Zhao, Oliver He
1236
genome of Gammaproteobacteria
The genome of an organism of Firmicutes
Bin Zhao, Oliver He
1239
genome of Firmicutes
The genome of an organism of Staphylococcus aureus
Bin Zhao, Oliver He
1280
genome of Staphylococcus aureus
The genome of an organism of Streptococcus
Bin Zhao, Oliver He
1301
genome of Streptococcus
The genome of an organism of Streptococcus agalactiae
Bin Zhao, Oliver He
1311
genome of Streptococcus agalactiae
The genome of an organism of Streptococcus pneumoniae
Bin Zhao, Oliver He
1313
genome of Streptococcus pneumoniae
The genome of an organism of Streptococcus pyogenes
Bin Zhao, Oliver He
1314
genome of Streptococcus pyogenes
The genome of an organism of Enterococcus
Bin Zhao, Oliver He
1350
genome of Enterococcus
The genome of an organism of Enterococcus faecalis
Bin Zhao, Oliver He
1351
genome of Enterococcus faecalis
The genome of an organism of Enterococcus faecium
Bin Zhao, Oliver He
1352
genome of Enterococcus faecium
The genome of an organism of Bacillales
Bin Zhao, Oliver He
1385
genome of Bacillales
The genome of an organism of Bacillus anthracis
Bin Zhao, Oliver He
1392
genome of Bacillus anthracis
The genome of an organism of Clostridium
Bin Zhao, Oliver He
1485
genome of Clostridium
The genome of an organism of Clostridium botulinum
Bin Zhao, Oliver He
1491
genome of Clostridium botulinum
The genome of an organism of [Clostridium] difficile
Bin Zhao, Oliver He
1496
genome of [Clostridium] difficile
The genome of an organism of Clostridium perfringens
Bin Zhao, Oliver He
1502
genome of Clostridium perfringens
The genome of an organism of Listeria monocytogenes
Bin Zhao, Oliver He
1639
genome of Listeria monocytogenes
The genome of an organism of Mycobacterium
Bin Zhao, Oliver He
1763
genome of Mycobacterium
The genome of an organism of Mycobacterium tuberculosis
Bin Zhao, Oliver He
1773
genome of Mycobacterium tuberculosis
The genome of an organism of Eukaryota
Bin Zhao, Oliver He
2759
genome of Eukaryota
The genome of an organism of Saccharomycetales
Bin Zhao, Oliver He
4892
genome of Saccharomycetales
The genome of an organism of Saccharomycetaceae
Bin Zhao, Oliver He
4893
genome of Saccharomycetaceae
The genome of an organism of Saccharomyces cerevisiae
Bin Zhao, Oliver He
4932
genome of Saccharomyces cerevisiae
The genome of an organism of Ajellomyces capsulatus
Bin Zhao, Oliver He
5037
genome of Ajellomyces capsulatus
The genome of an organism of Cryptococcus neoformans
Bin Zhao, Oliver He
5207
genome of Cryptococcus neoformans
The genome of an organism of Candida
Bin Zhao, Oliver He
5475
genome of Candida
The genome of an organism of Candida albicans
Bin Zhao, Oliver He
5476
genome of Candida albicans
The genome of an organism of Candida glabrata
Bin Zhao, Oliver He
5478
genome of Candida glabrata
The genome of an organism of Trypanosomatidae
Bin Zhao, Oliver He
5654
genome of Trypanosomatidae
The genome of an organism of Leishmania donovani
Bin Zhao, Oliver He
5661
genome of Leishmania donovani
The genome of an organism of Leishmania major
Bin Zhao, Oliver He
5664
genome of Leishmania major
The genome of an organism of Leishmania mexicana
Bin Zhao, Oliver He
5665
genome of Leishmania mexicana
The genome of an organism of Leishmania infantum
Bin Zhao, Oliver He
5671
genome of Leishmania infantum
The genome of an organism of Trypanosoma
Bin Zhao, Oliver He
5690
genome of Trypanosoma
The genome of an organism of Trypanosoma cruzi
Bin Zhao, Oliver He
5693
genome of Trypanosoma cruzi
The genome of an organism of Entamoeba histolytica
Bin Zhao, Oliver He
5759
genome of Entamoeba histolytica
The genome of an organism of Apicomplexa
Bin Zhao, Oliver He
5794
genome of Apicomplexa
The genome of an organism of Toxoplasma gondii
Bin Zhao, Oliver He
5811
genome of Toxoplasma gondii
The genome of an organism of Plasmodium
Bin Zhao, Oliver He
5820
genome of Plasmodium
The genome of an organism of Plasmodium berghei ANKA
Bin Zhao, Oliver He
5823
genome of Plasmodium berghei ANKA
The genome of an organism of Plasmodium yoelii
Bin Zhao, Oliver He
5861
genome of Plasmodium yoelii
The genome of an organism of Exophiala dermatitidis
Bin Zhao, Oliver He
5970
genome of Exophiala dermatitidis
The genome of an organism of Lythrurus
Bin Zhao, Oliver He
7966
genome of Lythrurus
The genome of an organism of Viruses
Bin Zhao, Oliver He
10239
genome of Viruses
The genome of an organism of Chordopoxvirinae
Bin Zhao, Oliver He
10241
genome of Chordopoxvirinae
The genome of an organism of Orthopoxvirus
Bin Zhao, Oliver He
10242
genome of Orthopoxvirus
The genome of an organism of Cowpox virus
Bin Zhao, Oliver He
10243
genome of Cowpox virus
The genome of an organism of Vaccinia virus
Bin Zhao, Oliver He
10245
genome of Vaccinia virus
The genome of an organism of Vaccinia virus Tian Tan
Bin Zhao, Oliver He
10253
genome of Vaccinia virus Tian Tan
The genome of an organism of Vaccinia virus WR
Bin Zhao, Oliver He
10254
genome of Vaccinia virus WR
The genome of an organism of Orf virus
Bin Zhao, Oliver He
10258
genome of Orf virus
The genome of an organism of Sheeppox virus
Bin Zhao, Oliver He
10266
genome of Sheeppox virus
The genome of an organism of Leporipoxvirus
Bin Zhao, Oliver He
10270
genome of Leporipoxvirus
The genome of an organism of Rabbit fibroma virus
Bin Zhao, Oliver He
10271
genome of Rabbit fibroma virus
The genome of an organism of Myxoma virus
Bin Zhao, Oliver He
10273
genome of Myxoma virus
The genome of an organism of Herpesviridae
Bin Zhao, Oliver He
10292
genome of Herpesviridae
The genome of an organism of Alphaherpesvirinae
Bin Zhao, Oliver He
10293
genome of Alphaherpesvirinae
The genome of an organism of Simplexvirus
Bin Zhao, Oliver He
10294
genome of Simplexvirus
The genome of an organism of Human herpesvirus 1
Bin Zhao, Oliver He
10298
genome of Human herpesvirus 1
The genome of an organism of Herpes simplex virus (type 1 / strain 17)
Bin Zhao, Oliver He
10299
genome of Herpes simplex virus (type 1 / strain 17)
The genome of an organism of Human herpesvirus 2
Bin Zhao, Oliver He
10310
genome of Human herpesvirus 2
The genome of an organism of Varicellovirus
Bin Zhao, Oliver He
10319
genome of Varicellovirus
The genome of an organism of Bovine herpesvirus 1
Bin Zhao, Oliver He
10320
genome of Bovine herpesvirus 1
The genome of an organism of Equid herpesvirus 1
Bin Zhao, Oliver He
10326
genome of Equid herpesvirus 1
The genome of an organism of Felid herpesvirus 1
Bin Zhao, Oliver He
10334
genome of Felid herpesvirus 1
The genome of an organism of Human herpesvirus 3
Bin Zhao, Oliver He
10335
genome of Human herpesvirus 3
The genome of an organism of Suid herpesvirus 1
Bin Zhao, Oliver He
10345
genome of Suid herpesvirus 1
The genome of an organism of Gallid herpesvirus 1
Bin Zhao, Oliver He
10386
genome of Gallid herpesvirus 1
The genome of an organism of Gallid herpesvirus 2
Bin Zhao, Oliver He
10390
genome of Gallid herpesvirus 2
The genome of an organism of African swine fever virus
Bin Zhao, Oliver He
10497
genome of African swine fever virus
The genome of an organism of Rotavirus
Bin Zhao, Oliver He
10912
genome of Rotavirus
The genome of an organism of Alphavirus
Bin Zhao, Oliver He
11019
genome of Alphavirus
The genome of an organism of Ross River virus
Bin Zhao, Oliver He
11029
genome of Ross River virus
The genome of an organism of Sindbis virus
Bin Zhao, Oliver He
11034
genome of Sindbis virus
The genome of an organism of Venezuelan equine encephalitis virus
Bin Zhao, Oliver He
11036
genome of Venezuelan equine encephalitis virus
The genome of an organism of Western equine encephalomyelitis virus
Bin Zhao, Oliver He
11039
genome of Western equine encephalomyelitis virus
The genome of an organism of Flaviviridae
Bin Zhao, Oliver He
11050
genome of Flaviviridae
The genome of an organism of Flavivirus
Bin Zhao, Oliver He
11051
genome of Flavivirus
The genome of an organism of West Nile virus
Bin Zhao, Oliver He
11082
genome of West Nile virus
The genome of an organism of Tick-borne encephalitis virus
Bin Zhao, Oliver He
11084
genome of Tick-borne encephalitis virus
The genome of an organism of Yellow fever virus
Bin Zhao, Oliver He
11089
genome of Yellow fever virus
The genome of an organism of Classical swine fever virus
Bin Zhao, Oliver He
11096
genome of Classical swine fever virus
The genome of an organism of Classical swine fever virus - Brescia
Bin Zhao, Oliver He
11098
genome of Classical swine fever virus - Brescia
The genome of an organism of Feline infectious peritonitis virus
Bin Zhao, Oliver He
11135
genome of Feline infectious peritonitis virus
The genome of an organism of Porcine respiratory coronavirus
Bin Zhao, Oliver He
11146
genome of Porcine respiratory coronavirus
The genome of an organism of Mononegavirales
Bin Zhao, Oliver He
11157
genome of Mononegavirales
The genome of an organism of Paramyxoviridae
Bin Zhao, Oliver He
11158
genome of Paramyxoviridae
The genome of an organism of Paramyxovirinae
Bin Zhao, Oliver He
11159
genome of Paramyxovirinae
The genome of an organism of Newcastle disease virus
Bin Zhao, Oliver He
11176
genome of Newcastle disease virus
The genome of an organism of Human parainfluenza virus 3
Bin Zhao, Oliver He
11216
genome of Human parainfluenza virus 3
The genome of an organism of Measles virus
Bin Zhao, Oliver He
11234
genome of Measles virus
The genome of an organism of Pneumovirinae
Bin Zhao, Oliver He
11244
genome of Pneumovirinae
The genome of an organism of Pneumovirus
Bin Zhao, Oliver He
11245
genome of Pneumovirus
The genome of an organism of Bovine respiratory syncytial virus
Bin Zhao, Oliver He
11246
genome of Bovine respiratory syncytial virus
The genome of an organism of Human respiratory syncytial virus A2
Bin Zhao, Oliver He
11259
genome of Human respiratory syncytial virus A2
The genome of an organism of Rhabdoviridae
Bin Zhao, Oliver He
11270
genome of Rhabdoviridae
The genome of an organism of Infectious hematopoietic necrosis virus
Bin Zhao, Oliver He
11290
genome of Infectious hematopoietic necrosis virus
The genome of an organism of Rabies virus
Bin Zhao, Oliver He
11292
genome of Rabies virus
The genome of an organism of Influenza A virus
Bin Zhao, Oliver He
11320
genome of Influenza A virus
The genome of an organism of Bunyaviridae
Bin Zhao, Oliver He
11571
genome of Bunyaviridae
The genome of an organism of La Crosse virus
Bin Zhao, Oliver He
11577
genome of La Crosse virus
The genome of an organism of Rift Valley fever virus
Bin Zhao, Oliver He
11588
genome of Rift Valley fever virus
The genome of an organism of Hantaan virus
Bin Zhao, Oliver He
11599
genome of Hantaan virus
The genome of an organism of Lentivirus
Bin Zhao, Oliver He
11646
genome of Lentivirus
The genome of an organism of Primate lentivirus group
Bin Zhao, Oliver He
11652
genome of Primate lentivirus group
The genome of an organism of Feline immunodeficiency virus
Bin Zhao, Oliver He
11673
genome of Feline immunodeficiency virus
The genome of an organism of Human immunodeficiency virus 1
Bin Zhao, Oliver He
11676
genome of Human immunodeficiency virus 1
The genome of an organism of Simian immunodeficiency virus
Bin Zhao, Oliver He
11723
genome of Simian immunodeficiency virus
The genome of an organism of Encephalomyocarditis virus
Bin Zhao, Oliver He
12104
genome of Encephalomyocarditis virus
The genome of an organism of Chicken anemia virus
Bin Zhao, Oliver He
12618
genome of Chicken anemia virus
The genome of an organism of Ectromelia virus
Bin Zhao, Oliver He
12643
genome of Ectromelia virus
The genome of an organism of Burkholderia mallei
Bin Zhao, Oliver He
13373
genome of Burkholderia mallei
The genome of an organism of Alphaproteobacteria
Bin Zhao, Oliver He
28211
genome of Alphaproteobacteria
The genome of an organism of Betaproteobacteria
Bin Zhao, Oliver He
28216
genome of Betaproteobacteria
The genome of an organism of Porcine reproductive and respiratory syndrome virus
Bin Zhao, Oliver He
28344
genome of Porcine reproductive and respiratory syndrome virus
The genome of an organism of Burkholderia pseudomallei
Bin Zhao, Oliver He
28450
genome of Burkholderia pseudomallei
The genome of an organism of Trichocomaceae
Bin Zhao, Oliver He
28568
genome of Trichocomaceae
The genome of an organism of Rotavirus A
Bin Zhao, Oliver He
28875
genome of Rotavirus A
The genome of an organism of Brucella melitensis
Bin Zhao, Oliver He
29459
genome of Brucella melitensis
The genome of an organism of Yersinia ruckeri
Bin Zhao, Oliver He
29486
genome of Yersinia ruckeri
The genome of an organism of Campylobacter jejuni subsp. jejuni
Bin Zhao, Oliver He
32022
genome of Campylobacter jejuni subsp. jejuni
The genome of an organism of Opisthokonta
Bin Zhao, Oliver He
33154
genome of Opisthokonta
The genome of an organism of Onygenales
Bin Zhao, Oliver He
33183
genome of Onygenales
The genome of an organism of Bilateria
Bin Zhao, Oliver He
33213
genome of Bilateria
The genome of an organism of Suid herpesvirus 1 strain Kaplan
Bin Zhao, Oliver He
33703
genome of Suid herpesvirus 1 strain Kaplan
The genome of an organism of Actinobacillus pleuropneumoniae serovar 2
Bin Zhao, Oliver He
34063
genome of Actinobacillus pleuropneumoniae serovar 2
The genome of an organism of dsDNA viruses, no RNA stage
Bin Zhao, Oliver He
35237
genome of dsDNA viruses, no RNA stage
The genome of an organism of Bovine herpesvirus 5
Bin Zhao, Oliver He
35244
genome of Bovine herpesvirus 5
The genome of an organism of ssRNA positive-strand viruses, no DNA stage
Bin Zhao, Oliver He
35278
genome of ssRNA positive-strand viruses, no DNA stage
The genome of an organism of ssRNA negative-strand viruses
Bin Zhao, Oliver He
35301
genome of ssRNA negative-strand viruses
The genome of an organism of Dictyochales
Bin Zhao, Oliver He
35685
genome of Dictyochales
The genome of an organism of Plasmodium falciparum 3D7
Bin Zhao, Oliver He
36329
genome of Plasmodium falciparum 3D7
The genome of an organism of Rotavirus C
Bin Zhao, Oliver He
36427
genome of Rotavirus C
The genome of an organism of Clostridium botulinum A
Bin Zhao, Oliver He
36826
genome of Clostridium botulinum A
The genome of an organism of Bartonella henselae
Bin Zhao, Oliver He
38323
genome of Bartonella henselae
The genome of an organism of Leishmania <subgenus>
Bin Zhao, Oliver He
38568
genome of Leishmania <subgenus>
The genome of an organism of Leishmania donovani species complex
Bin Zhao, Oliver He
38574
genome of Leishmania donovani species complex
The genome of an organism of Circoviridae
Bin Zhao, Oliver He
39724
genome of Circoviridae
The genome of an organism of Cryptococcus neoformans var. neoformans
Bin Zhao, Oliver He
40410
genome of Cryptococcus neoformans var. neoformans
The genome of an organism of Candida dubliniensis
Bin Zhao, Oliver He
42374
genome of Candida dubliniensis
The genome of an organism of Shigella flexneri 2a
Bin Zhao, Oliver He
42897
genome of Shigella flexneri 2a
The genome of an organism of Vibrio cholerae O139
Bin Zhao, Oliver He
45888
genome of Vibrio cholerae O139
The genome of an organism of Autographa californica nucleopolyhedrovirus
Bin Zhao, Oliver He
46015
genome of Autographa californica nucleopolyhedrovirus
The genome of an organism of Staphylococcus aureus subsp. aureus
Bin Zhao, Oliver He
46170
genome of Staphylococcus aureus subsp. aureus
The genome of an organism of Salmonella enterica subsp. enterica
Bin Zhao, Oliver He
59201
genome of Salmonella enterica subsp. enterica
The genome of an organism of Legionella pneumophila serogroup 1
Bin Zhao, Oliver He
66976
genome of Legionella pneumophila serogroup 1
The genome of an organism of Murine cytomegalovirus (strain K181)
Bin Zhao, Oliver He
69156
genome of Murine cytomegalovirus (strain K181)
The genome of an organism of Haemophilus influenzae Rd KW20
Bin Zhao, Oliver He
71421
genome of Haemophilus influenzae Rd KW20
The genome of an organism of Plasmodium yoelii yoelii
Bin Zhao, Oliver He
73239
genome of Plasmodium yoelii yoelii
The genome of an organism of Mannheimia haemolytica
Bin Zhao, Oliver He
75985
genome of Mannheimia haemolytica
The genome of an organism of Nidovirales
Bin Zhao, Oliver He
76804
genome of Nidovirales
The genome of an organism of Bovine herpesvirus type 1.1
Bin Zhao, Oliver He
79889
genome of Bovine herpesvirus type 1.1
The genome of an organism of Burkholderiales
Bin Zhao, Oliver He
80840
genome of Burkholderiales
The genome of an organism of Mycobacterium tuberculosis CDC1551
Bin Zhao, Oliver He
83331
genome of Mycobacterium tuberculosis CDC1551
The genome of an organism of Mycobacterium tuberculosis H37Rv
Bin Zhao, Oliver He
83332
genome of Mycobacterium tuberculosis H37Rv
The genome of an organism of Escherichia coli K-12
Bin Zhao, Oliver He
83333
genome of Escherichia coli K-12
The genome of an organism of Escherichia coli O157:H7
Bin Zhao, Oliver He
83334
genome of Escherichia coli O157:H7
The genome of an organism of Chlamydia pneumoniae
Bin Zhao, Oliver He
83558
genome of Chlamydia pneumoniae
The genome of an organism of Corynebacterineae
Bin Zhao, Oliver He
85007
genome of Corynebacterineae
The genome of an organism of Porcine circovirus 2
Bin Zhao, Oliver He
85708
genome of Porcine circovirus 2
The genome of an organism of Helicobacter pylori 26695
Bin Zhao, Oliver He
85962
genome of Helicobacter pylori 26695
The genome of an organism of Helicobacter pylori J99
Bin Zhao, Oliver He
85963
genome of Helicobacter pylori J99
The genome of an organism of Salmonella enterica subsp. enterica serovar Typhi
Bin Zhao, Oliver He
90370
genome of Salmonella enterica subsp. enterica serovar Typhi
The genome of an organism of Salmonella enterica subsp. enterica serovar Typhimurium
Bin Zhao, Oliver He
90371
genome of Salmonella enterica subsp. enterica serovar Typhimurium
The genome of an organism of Bacilli
Bin Zhao, Oliver He
91061
genome of Bacilli
The genome of an organism of Staphylococcus aureus subsp. aureus NCTC 8325
Bin Zhao, Oliver He
93061
genome of Staphylococcus aureus subsp. aureus NCTC 8325
The genome of an organism of Influenza A virus (A/Goose/Guangdong/1/96(H5N1))
Bin Zhao, Oliver He
93838
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
Bin Zhao, Oliver He
99287
genome of Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
The genome of an organism of H5N1 subtype
Bin Zhao, Oliver He
102793
genome of H5N1 subtype
The genome of an organism of Bartonella birtlesii
Bin Zhao, Oliver He
111504
genome of Bartonella birtlesii
The genome of an organism of pseudomallei group
Bin Zhao, Oliver He
111527
genome of pseudomallei group
The genome of an organism of Chlamydophila pneumoniae CWL029
Bin Zhao, Oliver He
115713
genome of Chlamydophila pneumoniae CWL029
The genome of an organism of Legionellales
Bin Zhao, Oliver He
118969
genome of Legionellales
The genome of an organism of Francisella tularensis subsp. holarctica
Bin Zhao, Oliver He
119857
genome of Francisella tularensis subsp. holarctica
The genome of an organism of Nipah virus
Bin Zhao, Oliver He
121791
genome of Nipah virus
The genome of an organism of Neisseria meningitidis MC58
Bin Zhao, Oliver He
122586
genome of Neisseria meningitidis MC58
The genome of an organism of Neisseria meningitidis Z2491
Bin Zhao, Oliver He
122587
genome of Neisseria meningitidis Z2491
The genome of an organism of Neisseria meningitidis serogroup C
Bin Zhao, Oliver He
135720
genome of Neisseria meningitidis serogroup C
The genome of an organism of Chlamydophila pneumoniae J138
Bin Zhao, Oliver He
138677
genome of Chlamydophila pneumoniae J138
The genome of an organism of Eurotiomycetes
Bin Zhao, Oliver He
147545
genome of Eurotiomycetes
The genome of an organism of Escherichia coli O157:H7 str. EDL933
Bin Zhao, Oliver He
155864
genome of Escherichia coli O157:H7 str. EDL933
The genome of an organism of Staphylococcus aureus subsp. aureus Mu50
Bin Zhao, Oliver He
158878
genome of Staphylococcus aureus subsp. aureus Mu50
The genome of an organism of Staphylococcus aureus subsp. aureus N315
Bin Zhao, Oliver He
158879
genome of Staphylococcus aureus subsp. aureus N315
The genome of an organism of Streptococcus pyogenes M1 GAS
Bin Zhao, Oliver He
160490
genome of Streptococcus pyogenes M1 GAS
The genome of an organism of Streptococcus pyogenes str. Manfredo
Bin Zhao, Oliver He
160491
genome of Streptococcus pyogenes str. Manfredo
The genome of an organism of Emericella nidulans
Bin Zhao, Oliver He
162425
genome of Emericella nidulans
The genome of an organism of Listeria monocytogenes EGD-e
Bin Zhao, Oliver He
169963
genome of Listeria monocytogenes EGD-e
The genome of an organism of Streptococcus pneumoniae TIGR4
Bin Zhao, Oliver He
170187
genome of Streptococcus pneumoniae TIGR4
The genome of an organism of Streptococcus pneumoniae R6
Bin Zhao, Oliver He
171101
genome of Streptococcus pneumoniae R6
The genome of an organism of Francisella tularensis subsp. tularensis SCHU S4
Bin Zhao, Oliver He
177416
genome of Francisella tularensis subsp. tularensis SCHU S4
The genome of an organism of WEEV complex
Bin Zhao, Oliver He
177874
genome of WEEV complex
The genome of an organism of Cryptococcus neoformans var. grubii
Bin Zhao, Oliver He
178876
genome of Cryptococcus neoformans var. grubii
The genome of an organism of Chlamydophila pneumoniae TW-183
Bin Zhao, Oliver He
182082
genome of Chlamydophila pneumoniae TW-183
The genome of an organism of Trypanosoma brucei TREU927
Bin Zhao, Oliver He
185431
genome of Trypanosoma brucei TREU927
The genome of an organism of Streptococcus pyogenes MGAS8232
Bin Zhao, Oliver He
186103
genome of Streptococcus pyogenes MGAS8232
The genome of an organism of Zaire ebolavirus
Bin Zhao, Oliver He
186538
genome of Zaire ebolavirus
The genome of an organism of Clostridiales
Bin Zhao, Oliver He
186802
genome of Clostridiales
The genome of an organism of Lactobacillales
Bin Zhao, Oliver He
186826
genome of Lactobacillales
The genome of an organism of Yersinia pestis KIM10+
Bin Zhao, Oliver He
187410
genome of Yersinia pestis KIM10+
The genome of an organism of Leptospira interrogans serovar Lai str. 56601
Bin Zhao, Oliver He
189518
genome of Leptospira interrogans serovar Lai str. 56601
The genome of an organism of Bacillus anthracis str. A2012
Bin Zhao, Oliver He
191218
genome of Bacillus anthracis str. A2012
The genome of an organism of Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
Bin Zhao, Oliver He
192222
genome of Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
The genome of an organism of Streptococcus pyogenes SSI-1
Bin Zhao, Oliver He
193567
genome of Streptococcus pyogenes SSI-1
The genome of an organism of Campylobacter jejuni RM1221
Bin Zhao, Oliver He
195099
genome of Campylobacter jejuni RM1221
The genome of an organism of Clostridium perfringens str. 13
Bin Zhao, Oliver He
195102
genome of Clostridium perfringens str. 13
The genome of an organism of Clostridium perfringens ATCC 13124
Bin Zhao, Oliver He
195103
genome of Clostridium perfringens ATCC 13124
The genome of an organism of Staphylococcus aureus subsp. aureus MW2
Bin Zhao, Oliver He
196620
genome of Staphylococcus aureus subsp. aureus MW2
The genome of an organism of Bacillus anthracis str. Ames
Bin Zhao, Oliver He
198094
genome of Bacillus anthracis str. Ames
The genome of an organism of Shigella flexneri 2a str. 301
Bin Zhao, Oliver He
198214
genome of Shigella flexneri 2a str. 301
The genome of an organism of Shigella flexneri 2a str. 2457T
Bin Zhao, Oliver He
198215
genome of Shigella flexneri 2a str. 2457T
The genome of an organism of Streptococcus pyogenes MGAS315
Bin Zhao, Oliver He
198466
genome of Streptococcus pyogenes MGAS315
The genome of an organism of Coccidioides posadasii
Bin Zhao, Oliver He
199306
genome of Coccidioides posadasii
The genome of an organism of Escherichia coli CFT073
Bin Zhao, Oliver He
199310
genome of Escherichia coli CFT073
The genome of an organism of Brucella suis 1330
Bin Zhao, Oliver He
204722
genome of Brucella suis 1330
The genome of an organism of Streptococcus agalactiae A909
Bin Zhao, Oliver He
205921
genome of Streptococcus agalactiae A909
The genome of an organism of Streptococcus agalactiae 2603V/R
Bin Zhao, Oliver He
208435
genome of Streptococcus agalactiae 2603V/R
The genome of an organism of Pseudomonas aeruginosa UCBPP-PA14
Bin Zhao, Oliver He
208963
genome of Pseudomonas aeruginosa UCBPP-PA14
The genome of an organism of Pseudomonas aeruginosa PAO1
Bin Zhao, Oliver He
208964
genome of Pseudomonas aeruginosa PAO1
The genome of an organism of Salmonella enterica subsp. enterica serovar Typhi str. Ty2
Bin Zhao, Oliver He
209261
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))
Bin Zhao, Oliver He
211044
genome of Influenza A virus (A/Puerto Rico/8/1934(H1N1))
The genome of an organism of Streptococcus agalactiae NEM316
Bin Zhao, Oliver He
211110
genome of Streptococcus agalactiae NEM316
The genome of an organism of Clostridium tetani E88
Bin Zhao, Oliver He
212717
genome of Clostridium tetani E88
The genome of an organism of Campylobacterales
Bin Zhao, Oliver He
213849
genome of Campylobacterales
The genome of an organism of Yersinia pestis CO92
Bin Zhao, Oliver He
214092
genome of Yersinia pestis CO92
The genome of an organism of Cryptococcus neoformans var. neoformans JEC21
Bin Zhao, Oliver He
214684
genome of Cryptococcus neoformans var. neoformans JEC21
The genome of an organism of Salmonella enterica subsp. enterica serovar Typhi str. CT18
Bin Zhao, Oliver He
220341
genome of Salmonella enterica subsp. enterica serovar Typhi str. CT18
The genome of an organism of Borrelia burgdorferi B31
Bin Zhao, Oliver He
224326
genome of Borrelia burgdorferi B31
The genome of an organism of Brucella melitensis bv. 1 str. 16M
Bin Zhao, Oliver He
224914
genome of Brucella melitensis bv. 1 str. 16M
The genome of an organism of Enterococcus faecalis V583
Bin Zhao, Oliver He
226185
genome of Enterococcus faecalis V583
The genome of an organism of Aspergillus nidulans FGSC A4
Bin Zhao, Oliver He
227321
genome of Aspergillus nidulans FGSC A4
The genome of an organism of Coxiella burnetii RSA 493
Bin Zhao, Oliver He
227377
genome of Coxiella burnetii RSA 493
The genome of an organism of Yersinia pestis biovar Microtus str. 91001
Bin Zhao, Oliver He
229193
genome of Yersinia pestis biovar Microtus str. 91001
The genome of an organism of Candida albicans SC5314
Bin Zhao, Oliver He
237561
genome of Candida albicans SC5314
The genome of an organism of Burkholderia mallei ATCC 23344
Bin Zhao, Oliver He
243160
genome of Burkholderia mallei ATCC 23344
The genome of an organism of Vibrio cholerae O1 biovar El Tor str. N16961
Bin Zhao, Oliver He
243277
genome of Vibrio cholerae O1 biovar El Tor str. N16961
The genome of an organism of Corynebacterium diphtheriae NCTC 13129
Bin Zhao, Oliver He
257309
genome of Corynebacterium diphtheriae NCTC 13129
The genome of an organism of Bordetella bronchiseptica RB50
Bin Zhao, Oliver He
257310
genome of Bordetella bronchiseptica RB50
The genome of an organism of Bordetella pertussis Tohama I
Bin Zhao, Oliver He
257313
genome of Bordetella pertussis Tohama I
The genome of an organism of Bacillus anthracis str. Sterne
Bin Zhao, Oliver He
260799
genome of Bacillus anthracis str. Sterne
The genome of an organism of Bacillus anthracis str. 'Ames Ancestor'
Bin Zhao, Oliver He
261594
genome of Bacillus anthracis str. 'Ames Ancestor'
The genome of an organism of Orgyia pseudotsugata MNPV
Bin Zhao, Oliver He
262177
genome of Orgyia pseudotsugata MNPV
The genome of an organism of Mycobacterium avium subsp. paratuberculosis K-10
Bin Zhao, Oliver He
262316
genome of Mycobacterium avium subsp. paratuberculosis K-10
The genome of an organism of Listeria monocytogenes serotype 4b str. F2365
Bin Zhao, Oliver He
265669
genome of Listeria monocytogenes serotype 4b str. F2365
The genome of an organism of Pneumonia virus of mice J3666
Bin Zhao, Oliver He
270473
genome of Pneumonia virus of mice J3666
The genome of an organism of Bombyx mori NPV
Bin Zhao, Oliver He
271108
genome of Bombyx mori NPV
The genome of an organism of Burkholderia pseudomallei K96243
Bin Zhao, Oliver He
272560
genome of Burkholderia pseudomallei K96243
The genome of an organism of Chlamydia trachomatis D/UW-3/CX
Bin Zhao, Oliver He
272561
genome of Chlamydia trachomatis D/UW-3/CX
The genome of an organism of Clostridium difficile 630
Bin Zhao, Oliver He
272563
genome of Clostridium difficile 630
The genome of an organism of Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Bin Zhao, Oliver He
272624
genome of Legionella pneumophila subsp. pneumophila str. Philadelphia 1
The genome of an organism of Neisseria meningitidis FAM18
Bin Zhao, Oliver He
272831
genome of Neisseria meningitidis FAM18
The genome of an organism of Pasteurella multocida subsp. multocida str. Pm70
Bin Zhao, Oliver He
272843
genome of Pasteurella multocida subsp. multocida str. Pm70
The genome of an organism of Rickettsia prowazekii str. Madrid E
Bin Zhao, Oliver He
272947
genome of Rickettsia prowazekii str. Madrid E
The genome of an organism of Staphylococcus aureus RF122
Bin Zhao, Oliver He
273036
genome of Staphylococcus aureus RF122
The genome of an organism of Yersinia pseudotuberculosis IP 32953
Bin Zhao, Oliver He
273123
genome of Yersinia pseudotuberculosis IP 32953
The genome of an organism of Haemophilus influenzae 86-028NP
Bin Zhao, Oliver He
281310
genome of Haemophilus influenzae 86-028NP
The genome of an organism of Staphylococcus aureus subsp. aureus MRSA252
Bin Zhao, Oliver He
282458
genome of Staphylococcus aureus subsp. aureus MRSA252
The genome of an organism of Bartonella henselae str. Houston-1
Bin Zhao, Oliver He
283166
genome of Bartonella henselae str. Houston-1
The genome of an organism of Cryptococcus neoformans var. neoformans B-3501A
Bin Zhao, Oliver He
283643
genome of Cryptococcus neoformans var. neoformans B-3501A
The genome of an organism of Influenza A virus (A/Viet Nam/1203/2004(H5N1))
Bin Zhao, Oliver He
284218
genome of Influenza A virus (A/Viet Nam/1203/2004(H5N1))
The genome of an organism of Candida glabrata CBS 138
Bin Zhao, Oliver He
284593
genome of Candida glabrata CBS 138
The genome of an organism of Streptococcus pyogenes MGAS10394
Bin Zhao, Oliver He
286636
genome of Streptococcus pyogenes MGAS10394
The genome of an organism of Clostridium perfringens SM101
Bin Zhao, Oliver He
289380
genome of Clostridium perfringens SM101
The genome of an organism of Streptococcus pyogenes MGAS5005
Bin Zhao, Oliver He
293653
genome of Streptococcus pyogenes MGAS5005
The genome of an organism of Entamoeba histolytica HM-1:IMSS
Bin Zhao, Oliver He
294381
genome of Entamoeba histolytica HM-1:IMSS
The genome of an organism of Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
Bin Zhao, Oliver He
295319
genome of Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
The genome of an organism of Legionella pneumophila str. Lens
Bin Zhao, Oliver He
297245
genome of Legionella pneumophila str. Lens
The genome of an organism of Legionella pneumophila str. Paris
Bin Zhao, Oliver He
297246
genome of Legionella pneumophila str. Paris
The genome of an organism of Shigella dysenteriae Sd197
Bin Zhao, Oliver He
300267
genome of Shigella dysenteriae Sd197
The genome of an organism of Shigella boydii Sb227
Bin Zhao, Oliver He
300268
genome of Shigella boydii Sb227
The genome of an organism of Shigella sonnei Ss046
Bin Zhao, Oliver He
300269
genome of Shigella sonnei Ss046
The genome of an organism of Streptococcus pyogenes serotype M1
Bin Zhao, Oliver He
301447
genome of Streptococcus pyogenes serotype M1
The genome of an organism of Streptococcus pyogenes serotype M3
Bin Zhao, Oliver He
301448
genome of Streptococcus pyogenes serotype M3
The genome of an organism of Escherichia coli str. K-12 substr. DH10B
Bin Zhao, Oliver He
316385
genome of Escherichia coli str. K-12 substr. DH10B
The genome of an organism of Escherichia coli ETEC H10407
Bin Zhao, Oliver He
316401
genome of Escherichia coli ETEC H10407
The genome of an organism of Streptococcus pyogenes MGAS6180
Bin Zhao, Oliver He
319701
genome of Streptococcus pyogenes MGAS6180
The genome of an organism of Burkholderia pseudomallei 1710b
Bin Zhao, Oliver He
320372
genome of Burkholderia pseudomallei 1710b
The genome of an organism of Burkholderia pseudomallei 668
Bin Zhao, Oliver He
320373
genome of Burkholderia pseudomallei 668
The genome of an organism of Burkholderia mallei SAVP1
Bin Zhao, Oliver He
320388
genome of Burkholderia mallei SAVP1
The genome of an organism of Burkholderia mallei NCTC 10247
Bin Zhao, Oliver He
320389
genome of Burkholderia mallei NCTC 10247
The genome of an organism of Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
Bin Zhao, Oliver He
321314
genome of Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
The genome of an organism of Aspergillus fumigatus Af293
Bin Zhao, Oliver He
330879
genome of Aspergillus fumigatus Af293
The genome of an organism of Escherichia coli E24377A
Bin Zhao, Oliver He
331111
genome of Escherichia coli E24377A
The genome of an organism of Escherichia coli HS
Bin Zhao, Oliver He
331112
genome of Escherichia coli HS
The genome of an organism of Mycobacterium tuberculosis F11
Bin Zhao, Oliver He
336982
genome of Mycobacterium tuberculosis F11
The genome of an organism of Streptococcus pyogenes serotype M12
Bin Zhao, Oliver He
342023
genome of Streptococcus pyogenes serotype M12
The genome of an organism of Shigella boydii CDC 3083-94
Bin Zhao, Oliver He
344609
genome of Shigella boydii CDC 3083-94
The genome of an organism of SARS coronavirus ZJ0301
Bin Zhao, Oliver He
344702
genome of SARS coronavirus ZJ0301
The genome of an organism of Vibrio cholerae O395
Bin Zhao, Oliver He
345073
genome of Vibrio cholerae O395
The genome of an organism of Leishmania major strain Friedlin
Bin Zhao, Oliver He
347515
genome of Leishmania major strain Friedlin
The genome of an organism of Yersinia pestis Angola
Bin Zhao, Oliver He
349746
genome of Yersinia pestis Angola
The genome of an organism of Yersinia pseudotuberculosis IP 31758
Bin Zhao, Oliver He
349747
genome of Yersinia pseudotuberculosis IP 31758
The genome of an organism of Plasmodium yoelii yoelii 17XNL
Bin Zhao, Oliver He
352914
genome of Plasmodium yoelii yoelii 17XNL
The genome of an organism of Cryptosporidium parvum Iowa II
Bin Zhao, Oliver He
353152
genome of Cryptosporidium parvum Iowa II
The genome of an organism of Trypanosoma cruzi strain CL Brener
Bin Zhao, Oliver He
353153
genome of Trypanosoma cruzi strain CL Brener
The genome of an organism of Campylobacter jejuni subsp. jejuni 81-176
Bin Zhao, Oliver He
354242
genome of Campylobacter jejuni subsp. jejuni 81-176
The genome of an organism of Burkholderia pseudomallei 1106a
Bin Zhao, Oliver He
357348
genome of Burkholderia pseudomallei 1106a
The genome of an organism of Brucella melitensis biovar Abortus 2308
Bin Zhao, Oliver He
359391
genome of Brucella melitensis biovar Abortus 2308
The genome of an organism of Bartonella bacilliformis KC583
Bin Zhao, Oliver He
360095
genome of Bartonella bacilliformis KC583
The genome of an organism of Yersinia pestis Antiqua
Bin Zhao, Oliver He
360102
genome of Yersinia pestis Antiqua
The genome of an organism of Campylobacter jejuni subsp. doylei 269.97
Bin Zhao, Oliver He
360109
genome of Campylobacter jejuni subsp. doylei 269.97
The genome of an organism of Bordetella avium 197N
Bin Zhao, Oliver He
360910
genome of Bordetella avium 197N
The genome of an organism of Escherichia coli 536
Bin Zhao, Oliver He
362663
genome of Escherichia coli 536
The genome of an organism of Escherichia coli UTI89
Bin Zhao, Oliver He
364106
genome of Escherichia coli UTI89
The genome of an organism of Streptococcus pyogenes MGAS9429
Bin Zhao, Oliver He
370551
genome of Streptococcus pyogenes MGAS9429
The genome of an organism of Streptococcus pyogenes MGAS10270
Bin Zhao, Oliver He
370552
genome of Streptococcus pyogenes MGAS10270
The genome of an organism of Streptococcus pyogenes MGAS2096
Bin Zhao, Oliver He
370553
genome of Streptococcus pyogenes MGAS2096
The genome of an organism of Streptococcus pyogenes MGAS10750
Bin Zhao, Oliver He
370554
genome of Streptococcus pyogenes MGAS10750
The genome of an organism of Streptococcus pneumoniae D39
Bin Zhao, Oliver He
373153
genome of Streptococcus pneumoniae D39
The genome of an organism of Shigella flexneri 5 str. 8401
Bin Zhao, Oliver He
373384
genome of Shigella flexneri 5 str. 8401
The genome of an organism of Neisseria meningitidis 053442
Bin Zhao, Oliver He
374833
genome of Neisseria meningitidis 053442
The genome of an organism of Francisella tularensis subsp. holarctica LVS
Bin Zhao, Oliver He
376619
genome of Francisella tularensis subsp. holarctica LVS
The genome of an organism of Escherichia coli O26:H-
Bin Zhao, Oliver He
376724
genome of Escherichia coli O26:H-
The genome of an organism of Yersinia pestis Nepal516
Bin Zhao, Oliver He
377628
genome of Yersinia pestis Nepal516
The genome of an organism of Aeromonas salmonicida subsp. salmonicida A449
Bin Zhao, Oliver He
382245
genome of Aeromonas salmonicida subsp. salmonicida A449
The genome of an organism of Bartonella tribocorum CIP 105476
Bin Zhao, Oliver He
382640
genome of Bartonella tribocorum CIP 105476
The genome of an organism of Escherichia coli O157:H7 str. Sakai
Bin Zhao, Oliver He
386585
genome of Escherichia coli O157:H7 str. Sakai
The genome of an organism of Yersinia pestis Pestoides F
Bin Zhao, Oliver He
386656
genome of Yersinia pestis Pestoides F
The genome of an organism of Yersinia enterocolitica subsp. enterocolitica 8081
Bin Zhao, Oliver He
393305
genome of Yersinia enterocolitica subsp. enterocolitica 8081
The genome of an organism of Legionella pneumophila str. Corby
Bin Zhao, Oliver He
400673
genome of Legionella pneumophila str. Corby
The genome of an organism of Escherichia coli APEC O1
Bin Zhao, Oliver He
405955
genome of Escherichia coli APEC O1
The genome of an organism of Campylobacter jejuni subsp. jejuni 81116
Bin Zhao, Oliver He
407148
genome of Campylobacter jejuni subsp. jejuni 81116
The genome of an organism of Escherichia coli SE11
Bin Zhao, Oliver He
409438
genome of Escherichia coli SE11
The genome of an organism of Burkholderia mallei NCTC 10229
Bin Zhao, Oliver He
412022
genome of Burkholderia mallei NCTC 10229
The genome of an organism of Yersinia pestis CA88-4125
Bin Zhao, Oliver He
412420
genome of Yersinia pestis CA88-4125
The genome of an organism of Escherichia coli B str. REL606
Bin Zhao, Oliver He
413997
genome of Escherichia coli B str. REL606
The genome of an organism of Actinobacillus pleuropneumoniae serovar 5b str. L20
Bin Zhao, Oliver He
416269
genome of Actinobacillus pleuropneumoniae serovar 5b str. L20
The genome of an organism of Plasmodium (Vinckeia)
Bin Zhao, Oliver He
418101
genome of Plasmodium (Vinckeia)
The genome of an organism of Staphylococcus aureus subsp. aureus Mu3
Bin Zhao, Oliver He
418127
genome of Staphylococcus aureus subsp. aureus Mu3
The genome of an organism of Mycobacterium tuberculosis H37Ra
Bin Zhao, Oliver He
419947
genome of Mycobacterium tuberculosis H37Ra
The genome of an organism of Eimeriorina
Bin Zhao, Oliver He
423054
genome of Eimeriorina
The genome of an organism of Legionella pneumophila 2300/99 Alcoy
Bin Zhao, Oliver He
423212
genome of Legionella pneumophila 2300/99 Alcoy
The genome of an organism of Staphylococcus aureus subsp. aureus str. Newman
Bin Zhao, Oliver He
426430
genome of Staphylococcus aureus subsp. aureus str. Newman
The genome of an organism of Actinobacillus pleuropneumoniae serovar 3 str. JL03
Bin Zhao, Oliver He
434271
genome of Actinobacillus pleuropneumoniae serovar 3 str. JL03
The genome of an organism of ssRNA viruses
Bin Zhao, Oliver He
439488
genome of ssRNA viruses
The genome of an organism of Escherichia coli SMS-3-5
Bin Zhao, Oliver He
439855
genome of Escherichia coli SMS-3-5
The genome of an organism of Clostridium botulinum A str. ATCC 19397
Bin Zhao, Oliver He
441770
genome of Clostridium botulinum A str. ATCC 19397
The genome of an organism of Clostridium botulinum A str. Hall
Bin Zhao, Oliver He
441771
genome of Clostridium botulinum A str. Hall
The genome of an organism of Escherichia coli O157:H7 str. EC4115
Bin Zhao, Oliver He
444450
genome of Escherichia coli O157:H7 str. EC4115
The genome of an organism of Borrelia burgdorferi 156a
Bin Zhao, Oliver He
445983
genome of Borrelia burgdorferi 156a
The genome of an organism of Borrelia burgdorferi ZS7
Bin Zhao, Oliver He
445985
genome of Borrelia burgdorferi ZS7
The genome of an organism of Dikarya
Bin Zhao, Oliver He
451864
genome of Dikarya
The genome of an organism of Eurotiomycetidae
Bin Zhao, Oliver He
451871
genome of Eurotiomycetidae
The genome of an organism of Francisella tularensis subsp. holarctica FTNF002-00
Bin Zhao, Oliver He
458234
genome of Francisella tularensis subsp. holarctica FTNF002-00
The genome of an organism of Streptococcus pyogenes NZ131
Bin Zhao, Oliver He
471876
genome of Streptococcus pyogenes NZ131
The genome of an organism of Enterococcus faecalis OG1RF
Bin Zhao, Oliver He
474186
genome of Enterococcus faecalis OG1RF
The genome of an organism of Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
Bin Zhao, Oliver He
476213
genome of Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
The genome of an organism of Paenibacillus sp. Y412MC10
Bin Zhao, Oliver He
481743
genome of Paenibacillus sp. Y412MC10
The genome of an organism of Streptococcus pneumoniae Taiwan19F-14
Bin Zhao, Oliver He
487213
genome of Streptococcus pneumoniae Taiwan19F-14
The genome of an organism of Streptococcus pneumoniae Hungary19A-6
Bin Zhao, Oliver He
487214
genome of Streptococcus pneumoniae Hungary19A-6
The genome of an organism of Streptococcus pneumoniae 70585
Bin Zhao, Oliver He
488221
genome of Streptococcus pneumoniae 70585
The genome of an organism of Streptococcus pneumoniae JJA
Bin Zhao, Oliver He
488222
genome of Streptococcus pneumoniae JJA
The genome of an organism of Streptococcus pneumoniae P1031
Bin Zhao, Oliver He
488223
genome of Streptococcus pneumoniae P1031
The genome of an organism of Clostridium botulinum B1 str. Okra
Bin Zhao, Oliver He
498213
genome of Clostridium botulinum B1 str. Okra
The genome of an organism of Clostridium botulinum A3 str. Loch Maree
Bin Zhao, Oliver He
498214
genome of Clostridium botulinum A3 str. Loch Maree
The genome of an organism of Edwardsiella tarda EIB202
Bin Zhao, Oliver He
498217
genome of Edwardsiella tarda EIB202
The genome of an organism of Yersinia pseudotuberculosis YPIII
Bin Zhao, Oliver He
502800
genome of Yersinia pseudotuberculosis YPIII
The genome of an organism of Yersinia pseudotuberculosis PB1/+
Bin Zhao, Oliver He
502801
genome of Yersinia pseudotuberculosis PB1/+
The genome of an organism of Clostridium botulinum E3 str. Alaska E43
Bin Zhao, Oliver He
508767
genome of Clostridium botulinum E3 str. Alaska E43
The genome of an organism of Toxoplasma gondii ME49
Bin Zhao, Oliver He
508771
genome of Toxoplasma gondii ME49
The genome of an organism of Escherichia coli str. K-12 substr. MG1655
Bin Zhao, Oliver He
511145
genome of Escherichia coli str. K-12 substr. MG1655
The genome of an organism of Streptococcus pneumoniae G54
Bin Zhao, Oliver He
512566
genome of Streptococcus pneumoniae G54
The genome of an organism of Streptococcus pneumoniae CGSP14
Bin Zhao, Oliver He
516950
genome of Streptococcus pneumoniae CGSP14
The genome of an organism of Borrelia burgdorferi N40
Bin Zhao, Oliver He
521007
genome of Borrelia burgdorferi N40
The genome of an organism of Borrelia burgdorferi 297
Bin Zhao, Oliver He
521009
genome of Borrelia burgdorferi 297
The genome of an organism of Burkholderia pseudomallei MSHR346
Bin Zhao, Oliver He
536230
genome of Burkholderia pseudomallei MSHR346
The genome of an organism of Actinobacillus pleuropneumoniae serovar 7 str. AP76
Bin Zhao, Oliver He
537457
genome of Actinobacillus pleuropneumoniae serovar 7 str. AP76
The genome of an organism of Escherichia coli O157:H7 str. TW14359
Bin Zhao, Oliver He
544404
genome of Escherichia coli O157:H7 str. TW14359
The genome of an organism of Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
Bin Zhao, Oliver He
550537
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
Bin Zhao, Oliver He
550538
genome of Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91
The genome of an organism of Filobasidiella/Cryptococcus neoformans species complex
Bin Zhao, Oliver He
552466
genome of Filobasidiella/Cryptococcus neoformans species complex
The genome of an organism of Cryptococcus gattii
Bin Zhao, Oliver He
552467
genome of Cryptococcus gattii
The genome of an organism of Streptococcus equi subsp. zooepidemicus MGCS10565
Bin Zhao, Oliver He
552526
genome of Streptococcus equi subsp. zooepidemicus MGCS10565
The genome of an organism of Listeria monocytogenes HCC23
Bin Zhao, Oliver He
552536
genome of Listeria monocytogenes HCC23
The genome of an organism of Pseudomonas aeruginosa LESB58
Bin Zhao, Oliver He
557722
genome of Pseudomonas aeruginosa LESB58
The genome of an organism of Alphabaculovirus
Bin Zhao, Oliver He
558016
genome of Alphabaculovirus
The genome of an organism of Saccharomyces cerevisiae S288c
Bin Zhao, Oliver He
559292
genome of Saccharomyces cerevisiae S288c
The genome of an organism of Streptococcus pneumoniae ATCC 700669
Bin Zhao, Oliver He
561276
genome of Streptococcus pneumoniae ATCC 700669
The genome of an organism of Helicobacter pylori G27
Bin Zhao, Oliver He
563041
genome of Helicobacter pylori G27
The genome of an organism of Listeria monocytogenes L99
Bin Zhao, Oliver He
563174
genome of Listeria monocytogenes L99
The genome of an organism of Escherichia coli Vir68
Bin Zhao, Oliver He
563770
genome of Escherichia coli Vir68
The genome of an organism of Bacillus anthracis str. CDC 684
Bin Zhao, Oliver He
568206
genome of Bacillus anthracis str. CDC 684
The genome of an organism of Listeria monocytogenes serotype 4b str. CLIP 80459
Bin Zhao, Oliver He
568819
genome of Listeria monocytogenes serotype 4b str. CLIP 80459
The genome of an organism of Helicobacter pylori P12
Bin Zhao, Oliver He
570508
genome of Helicobacter pylori P12
The genome of an organism of Escherichia coli O26:H11 str. 11368
Bin Zhao, Oliver He
573235
genome of Escherichia coli O26:H11 str. 11368
The genome of an organism of Escherichia coli O127:H6 str. E2348/69
Bin Zhao, Oliver He
574521
genome of Escherichia coli O127:H6 str. E2348/69
The genome of an organism of Vibrio cholerae M66-2
Bin Zhao, Oliver He
579112
genome of Vibrio cholerae M66-2
The genome of an organism of Escherichia coli IAI1
Bin Zhao, Oliver He
585034
genome of Escherichia coli IAI1
The genome of an organism of Escherichia coli S88
Bin Zhao, Oliver He
585035
genome of Escherichia coli S88
The genome of an organism of Escherichia coli 55989
Bin Zhao, Oliver He
585055
genome of Escherichia coli 55989
The genome of an organism of Escherichia coli UMN026
Bin Zhao, Oliver He
585056
genome of Escherichia coli UMN026
The genome of an organism of Escherichia coli IAI39
Bin Zhao, Oliver He
585057
genome of Escherichia coli IAI39
The genome of an organism of Escherichia coli O103:H2 str. 12009
Bin Zhao, Oliver He
585395
genome of Escherichia coli O103:H2 str. 12009
The genome of an organism of Escherichia coli O111:H- str. 11128
Bin Zhao, Oliver He
585396
genome of Escherichia coli O111:H- str. 11128
The genome of an organism of Escherichia coli ED1a
Bin Zhao, Oliver He
585397
genome of Escherichia coli ED1a
The genome of an organism of Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
Bin Zhao, Oliver He
588858
genome of Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
The genome of an organism of Bacillus anthracis str. A0248
Bin Zhao, Oliver He
592021
genome of Bacillus anthracis str. A0248
The genome of an organism of Helicobacter pylori B38
Bin Zhao, Oliver He
592205
genome of Helicobacter pylori B38
The genome of an organism of Escherichia coli BW2952
Bin Zhao, Oliver He
595496
genome of Escherichia coli BW2952
The genome of an organism of SARS coronavirus ExoN1
Bin Zhao, Oliver He
627440
genome of SARS coronavirus ExoN1
The genome of an organism of Listeria monocytogenes 08-5923
Bin Zhao, Oliver He
637381
genome of Listeria monocytogenes 08-5923
The genome of an organism of Listeria monocytogenes 08-5578
Bin Zhao, Oliver He
653938
genome of Listeria monocytogenes 08-5578
The genome of an organism of Neisseria meningitidis alpha14
Bin Zhao, Oliver He
662598
genome of Neisseria meningitidis alpha14
The genome of an organism of Staphylococcus aureus subsp. aureus ED98
Bin Zhao, Oliver He
681288
genome of Staphylococcus aureus subsp. aureus ED98
The genome of an organism of Coronavirinae
Bin Zhao, Oliver He
693995
genome of Coronavirinae
The genome of an organism of Alphacoronavirus 1
Bin Zhao, Oliver He
693997
genome of Alphacoronavirus 1
The genome of an organism of Severe acute respiratory syndrome-related coronavirus
Bin Zhao, Oliver He
694009
genome of Severe acute respiratory syndrome-related coronavirus
The genome of an organism of Human metapneumovirus CAN97-83
Bin Zhao, Oliver He
694067
genome of Human metapneumovirus CAN97-83
The genome of an organism of Mileewa branchiuma
Bin Zhao, Oliver He
700720
genome of Mileewa branchiuma
The genome of an organism of Staphylococcus aureus 04-02981
Bin Zhao, Oliver He
703339
genome of Staphylococcus aureus 04-02981
The genome of an organism of Mycoplasma gallisepticum str. R(low)
Bin Zhao, Oliver He
710127
genome of Mycoplasma gallisepticum str. R(low)
The genome of an organism of saccharomyceta
Bin Zhao, Oliver He
716545
genome of saccharomyceta
The genome of an organism of Legionella pneumophila 130b
Bin Zhao, Oliver He
866628
genome of Legionella pneumophila 130b
The genome of an organism of Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74
Bin Zhao, Oliver He
909946
genome of Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74
A gene of an organism of Bacteria
Bin Zhao, Oliver He
2
gene of Bacteria
A gene of an organism of Spirochaetales
Bin Zhao, Oliver He
136
gene of Spirochaetales
A gene of an organism of Borrelia burgdorferi
Bin Zhao, Oliver He
139
gene of Borrelia burgdorferi
A gene of an organism of Campylobacter jejuni
Bin Zhao, Oliver He
197
gene of Campylobacter jejuni
A gene of an organism of Helicobacter pylori
Bin Zhao, Oliver He
210
gene of Helicobacter pylori
A gene of an organism of Brucella
Bin Zhao, Oliver He
234
gene of Brucella
A gene of an organism of Brucella abortus
Bin Zhao, Oliver He
235
gene of Brucella abortus
A gene of an organism of Francisella tularensis
Bin Zhao, Oliver He
263
gene of Francisella tularensis
A gene of an organism of Pseudomonas aeruginosa
Bin Zhao, Oliver He
287
gene of Pseudomonas aeruginosa
A gene of an organism of Rhizobiales
Bin Zhao, Oliver He
356
gene of Rhizobiales
A gene of an organism of Legionella pneumophila
Bin Zhao, Oliver He
446
gene of Legionella pneumophila
A gene of an organism of Neisseria meningitidis
Bin Zhao, Oliver He
487
gene of Neisseria meningitidis
A gene of an organism of Bordetella
Bin Zhao, Oliver He
517
gene of Bordetella
A gene of an organism of Bordetella pertussis
Bin Zhao, Oliver He
520
gene of Bordetella pertussis
A gene of an organism of Enterobacteriaceae
Bin Zhao, Oliver He
543
gene of Enterobacteriaceae
A gene of an organism of Escherichia coli
Bin Zhao, Oliver He
562
gene of Escherichia coli
A gene of an organism of Shigella
Bin Zhao, Oliver He
620
gene of Shigella
A gene of an organism of Shigella boydii
Bin Zhao, Oliver He
621
gene of Shigella boydii
A gene of an organism of Shigella flexneri
Bin Zhao, Oliver He
623
gene of Shigella flexneri
A gene of an organism of Yersinia <bacteria>
Bin Zhao, Oliver He
629
gene of Yersinia <bacteria>
A gene of an organism of Yersinia enterocolitica
Bin Zhao, Oliver He
630
gene of Yersinia enterocolitica
A gene of an organism of Yersinia pestis
Bin Zhao, Oliver He
632
gene of Yersinia pestis
A gene of an organism of Yersinia pseudotuberculosis
Bin Zhao, Oliver He
633
gene of Yersinia pseudotuberculosis
A gene of an organism of Vibrio cholerae
Bin Zhao, Oliver He
666
gene of Vibrio cholerae
A gene of an organism of Pasteurellaceae
Bin Zhao, Oliver He
712
gene of Pasteurellaceae
A gene of an organism of Actinobacillus pleuropneumoniae
Bin Zhao, Oliver He
715
gene of Actinobacillus pleuropneumoniae
A gene of an organism of Haemophilus influenzae
Bin Zhao, Oliver He
727
gene of Haemophilus influenzae
A gene of an organism of Pasteurella multocida
Bin Zhao, Oliver He
747
gene of Pasteurella multocida
A gene of an organism of Bartonella
Bin Zhao, Oliver He
773
gene of Bartonella
A gene of an organism of Chlamydia
Bin Zhao, Oliver He
810
gene of Chlamydia
A gene of an organism of Proteobacteria
Bin Zhao, Oliver He
1224
gene of Proteobacteria
A gene of an organism of Gammaproteobacteria
Bin Zhao, Oliver He
1236
gene of Gammaproteobacteria
A gene of an organism of Firmicutes
Bin Zhao, Oliver He
1239
gene of Firmicutes
A gene of an organism of Staphylococcus aureus
Bin Zhao, Oliver He
1280
gene of Staphylococcus aureus
A gene of an organism of Streptococcus
Bin Zhao, Oliver He
1301
gene of Streptococcus
A gene of an organism of Streptococcus agalactiae
Bin Zhao, Oliver He
1311
gene of Streptococcus agalactiae
A gene of an organism of Streptococcus pneumoniae
Bin Zhao, Oliver He
1313
gene of Streptococcus pneumoniae
A gene of an organism of Streptococcus pyogenes
Bin Zhao, Oliver He
1314
gene of Streptococcus pyogenes
A gene of an organism of Enterococcus
Bin Zhao, Oliver He
1350
gene of Enterococcus
A gene of an organism of Enterococcus faecalis
Bin Zhao, Oliver He
1351
gene of Enterococcus faecalis
A gene of an organism of Enterococcus faecium
Bin Zhao, Oliver He
1352
gene of Enterococcus faecium
A gene of an organism of Bacillales
Bin Zhao, Oliver He
1385
gene of Bacillales
A gene of an organism of Bacillus anthracis
Bin Zhao, Oliver He
1392
gene of Bacillus anthracis
A gene of an organism of Clostridium
Bin Zhao, Oliver He
1485
gene of Clostridium
A gene of an organism of Clostridium botulinum
Bin Zhao, Oliver He
1491
gene of Clostridium botulinum
A gene of an organism of [Clostridium] difficile
Bin Zhao, Oliver He
1496
gene of [Clostridium] difficile
A gene of an organism of Clostridium perfringens
Bin Zhao, Oliver He
1502
gene of Clostridium perfringens
A gene of an organism of Listeria monocytogenes
Bin Zhao, Oliver He
1639
gene of Listeria monocytogenes
A gene of an organism of Mycobacterium
Bin Zhao, Oliver He
1763
gene of Mycobacterium
A gene of an organism of Mycobacterium tuberculosis
Bin Zhao, Oliver He
1773
gene of Mycobacterium tuberculosis
A gene of an organism of Eukaryota
Bin Zhao, Oliver He
2759
gene of Eukaryota
A gene of an organism of Saccharomycetales
Bin Zhao, Oliver He
4892
gene of Saccharomycetales
A gene of an organism of Saccharomycetaceae
Bin Zhao, Oliver He
4893
gene of Saccharomycetaceae
A gene of an organism of Saccharomyces cerevisiae
Bin Zhao, Oliver He
4932
gene of Saccharomyces cerevisiae
A gene of an organism of Ajellomyces capsulatus
Bin Zhao, Oliver He
5037
gene of Ajellomyces capsulatus
A gene of an organism of Cryptococcus neoformans
Bin Zhao, Oliver He
5207
gene of Cryptococcus neoformans
A gene of an organism of Candida
Bin Zhao, Oliver He
5475
gene of Candida
A gene of an organism of Candida albicans
Bin Zhao, Oliver He
5476
gene of Candida albicans
A gene of an organism of Candida glabrata
Bin Zhao, Oliver He
5478
gene of Candida glabrata
A gene of an organism of Trypanosomatidae
Bin Zhao, Oliver He
5654
gene of Trypanosomatidae
A gene of an organism of Leishmania donovani
Bin Zhao, Oliver He
5661
gene of Leishmania donovani
A gene of an organism of Leishmania major
Bin Zhao, Oliver He
5664
gene of Leishmania major
A gene of an organism of Leishmania mexicana
Bin Zhao, Oliver He
5665
gene of Leishmania mexicana
A gene of an organism of Leishmania infantum
Bin Zhao, Oliver He
5671
gene of Leishmania infantum
A gene of an organism of Trypanosoma
Bin Zhao, Oliver He
5690
gene of Trypanosoma
A gene of an organism of Trypanosoma cruzi
Bin Zhao, Oliver He
5693
gene of Trypanosoma cruzi
A gene of an organism of Entamoeba histolytica
Bin Zhao, Oliver He
5759
gene of Entamoeba histolytica
A gene of an organism of Apicomplexa
Bin Zhao, Oliver He
5794
gene of Apicomplexa
A gene of an organism of Toxoplasma gondii
Bin Zhao, Oliver He
5811
gene of Toxoplasma gondii
A gene of an organism of Plasmodium
Bin Zhao, Oliver He
5820
gene of Plasmodium
A gene of an organism of Plasmodium berghei ANKA
Bin Zhao, Oliver He
5823
gene of Plasmodium berghei ANKA
A gene of an organism of Plasmodium yoelii
Bin Zhao, Oliver He
5861
gene of Plasmodium yoelii
A gene of an organism of Exophiala dermatitidis
Bin Zhao, Oliver He
5970
gene of Exophiala dermatitidis
A gene of an organism of Lythrurus
Bin Zhao, Oliver He
7966
gene of Lythrurus
A gene of an organism of Viruses
Bin Zhao, Oliver He
10239
gene of Viruses
A gene of an organism of Chordopoxvirinae
Bin Zhao, Oliver He
10241
gene of Chordopoxvirinae
A gene of an organism of Orthopoxvirus
Bin Zhao, Oliver He
10242
gene of Orthopoxvirus
A gene of an organism of Cowpox virus
Bin Zhao, Oliver He
10243
gene of Cowpox virus
A gene of an organism of Vaccinia virus
Bin Zhao, Oliver He
10245
gene of Vaccinia virus
A gene of an organism of Vaccinia virus Tian Tan
Bin Zhao, Oliver He
10253
gene of Vaccinia virus Tian Tan
A gene of an organism of Vaccinia virus WR
Bin Zhao, Oliver He
10254
gene of Vaccinia virus WR
A gene of an organism of Orf virus
Bin Zhao, Oliver He
10258
gene of Orf virus
A gene of an organism of Sheeppox virus
Bin Zhao, Oliver He
10266
gene of Sheeppox virus
A gene of an organism of Leporipoxvirus
Bin Zhao, Oliver He
10270
gene of Leporipoxvirus
A gene of an organism of Rabbit fibroma virus
Bin Zhao, Oliver He
10271
gene of Rabbit fibroma virus
A gene of an organism of Myxoma virus
Bin Zhao, Oliver He
10273
gene of Myxoma virus
A gene of an organism of Herpesviridae
Bin Zhao, Oliver He
10292
gene of Herpesviridae
A gene of an organism of Alphaherpesvirinae
Bin Zhao, Oliver He
10293
gene of Alphaherpesvirinae
A gene of an organism of Simplexvirus
Bin Zhao, Oliver He
10294
gene of Simplexvirus
A gene of an organism of Human herpesvirus 1
Bin Zhao, Oliver He
10298
gene of Human herpesvirus 1
A gene of an organism of Herpes simplex virus (type 1 / strain 17)
Bin Zhao, Oliver He
10299
gene of Herpes simplex virus (type 1 / strain 17)
A gene of an organism of Human herpesvirus 2
Bin Zhao, Oliver He
10310
gene of Human herpesvirus 2
A gene of an organism of Varicellovirus
Bin Zhao, Oliver He
10319
gene of Varicellovirus
A gene of an organism of Bovine herpesvirus 1
Bin Zhao, Oliver He
10320
gene of Bovine herpesvirus 1
A gene of an organism of Equid herpesvirus 1
Bin Zhao, Oliver He
10326
gene of Equid herpesvirus 1
A gene of an organism of Felid herpesvirus 1
Bin Zhao, Oliver He
10334
gene of Felid herpesvirus 1
A gene of an organism of Human herpesvirus 3
Bin Zhao, Oliver He
10335
gene of Human herpesvirus 3
A gene of an organism of Suid herpesvirus 1
Bin Zhao, Oliver He
10345
gene of Suid herpesvirus 1
A gene of an organism of Gallid herpesvirus 1
Bin Zhao, Oliver He
10386
gene of Gallid herpesvirus 1
A gene of an organism of Gallid herpesvirus 2
Bin Zhao, Oliver He
10390
gene of Gallid herpesvirus 2
A gene of an organism of African swine fever virus
Bin Zhao, Oliver He
10497
gene of African swine fever virus
A gene of an organism of Rotavirus
Bin Zhao, Oliver He
10912
gene of Rotavirus
A gene of an organism of Alphavirus
Bin Zhao, Oliver He
11019
gene of Alphavirus
A gene of an organism of Ross River virus
Bin Zhao, Oliver He
11029
gene of Ross River virus
A gene of an organism of Sindbis virus
Bin Zhao, Oliver He
11034
gene of Sindbis virus
A gene of an organism of Venezuelan equine encephalitis virus
Bin Zhao, Oliver He
11036
gene of Venezuelan equine encephalitis virus
A gene of an organism of Western equine encephalomyelitis virus
Bin Zhao, Oliver He
11039
gene of Western equine encephalomyelitis virus
A gene of an organism of Flaviviridae
Bin Zhao, Oliver He
11050
gene of Flaviviridae
A gene of an organism of Flavivirus
Bin Zhao, Oliver He
11051
gene of Flavivirus
A gene of an organism of West Nile virus
Bin Zhao, Oliver He
11082
gene of West Nile virus
A gene of an organism of Tick-borne encephalitis virus
Bin Zhao, Oliver He
11084
gene of Tick-borne encephalitis virus
A gene of an organism of Yellow fever virus
Bin Zhao, Oliver He
11089
gene of Yellow fever virus
A gene of an organism of Classical swine fever virus
Bin Zhao, Oliver He
11096
gene of Classical swine fever virus
A gene of an organism of Classical swine fever virus - Brescia
Bin Zhao, Oliver He
11098
gene of Classical swine fever virus - Brescia
A gene of an organism of Feline infectious peritonitis virus
Bin Zhao, Oliver He
11135
gene of Feline infectious peritonitis virus
A gene of an organism of Porcine respiratory coronavirus
Bin Zhao, Oliver He
11146
gene of Porcine respiratory coronavirus
A gene of an organism of Mononegavirales
Bin Zhao, Oliver He
11157
gene of Mononegavirales
A gene of an organism of Paramyxoviridae
Bin Zhao, Oliver He
11158
gene of Paramyxoviridae
A gene of an organism of Paramyxovirinae
Bin Zhao, Oliver He
11159
gene of Paramyxovirinae
A gene of an organism of Newcastle disease virus
Bin Zhao, Oliver He
11176
gene of Newcastle disease virus
A gene of an organism of Human parainfluenza virus 3
Bin Zhao, Oliver He
11216
gene of Human parainfluenza virus 3
A gene of an organism of Measles virus
Bin Zhao, Oliver He
11234
gene of Measles virus
A gene of an organism of Pneumovirinae
Bin Zhao, Oliver He
11244
gene of Pneumovirinae
A gene of an organism of Pneumovirus
Bin Zhao, Oliver He
11245
gene of Pneumovirus
A gene of an organism of Bovine respiratory syncytial virus
Bin Zhao, Oliver He
11246
gene of Bovine respiratory syncytial virus
A gene of an organism of Human respiratory syncytial virus A2
Bin Zhao, Oliver He
11259
gene of Human respiratory syncytial virus A2
A gene of an organism of Rhabdoviridae
Bin Zhao, Oliver He
11270
gene of Rhabdoviridae
A gene of an organism of Infectious hematopoietic necrosis virus
Bin Zhao, Oliver He
11290
gene of Infectious hematopoietic necrosis virus
A gene of an organism of Rabies virus
Bin Zhao, Oliver He
11292
gene of Rabies virus
A gene of an organism of Influenza A virus
Bin Zhao, Oliver He
11320
gene of Influenza A virus
A gene of an organism of Bunyaviridae
Bin Zhao, Oliver He
11571
gene of Bunyaviridae
A gene of an organism of La Crosse virus
Bin Zhao, Oliver He
11577
gene of La Crosse virus
A gene of an organism of Rift Valley fever virus
Bin Zhao, Oliver He
11588
gene of Rift Valley fever virus
A gene of an organism of Hantaan virus
Bin Zhao, Oliver He
11599
gene of Hantaan virus
A gene of an organism of Lentivirus
Bin Zhao, Oliver He
11646
gene of Lentivirus
A gene of an organism of Primate lentivirus group
Bin Zhao, Oliver He
11652
gene of Primate lentivirus group
A gene of an organism of Feline immunodeficiency virus
Bin Zhao, Oliver He
11673
gene of Feline immunodeficiency virus
A gene of an organism of Human immunodeficiency virus 1
Bin Zhao, Oliver He
11676
gene of Human immunodeficiency virus 1
A gene of an organism of Simian immunodeficiency virus
Bin Zhao, Oliver He
11723
gene of Simian immunodeficiency virus
A gene of an organism of Encephalomyocarditis virus
Bin Zhao, Oliver He
12104
gene of Encephalomyocarditis virus
A gene of an organism of Chicken anemia virus
Bin Zhao, Oliver He
12618
gene of Chicken anemia virus
A gene of an organism of Ectromelia virus
Bin Zhao, Oliver He
12643
gene of Ectromelia virus
A gene of an organism of Burkholderia mallei
Bin Zhao, Oliver He
13373
gene of Burkholderia mallei
A gene of an organism of Alphaproteobacteria
Bin Zhao, Oliver He
28211
gene of Alphaproteobacteria
A gene of an organism of Betaproteobacteria
Bin Zhao, Oliver He
28216
gene of Betaproteobacteria
A gene of an organism of Porcine reproductive and respiratory syndrome virus
Bin Zhao, Oliver He
28344
gene of Porcine reproductive and respiratory syndrome virus
A gene of an organism of Burkholderia pseudomallei
Bin Zhao, Oliver He
28450
gene of Burkholderia pseudomallei
A gene of an organism of Trichocomaceae
Bin Zhao, Oliver He
28568
gene of Trichocomaceae
A gene of an organism of Rotavirus A
Bin Zhao, Oliver He
28875
gene of Rotavirus A
A gene of an organism of Brucella melitensis
Bin Zhao, Oliver He
29459
gene of Brucella melitensis
A gene of an organism of Yersinia ruckeri
Bin Zhao, Oliver He
29486
gene of Yersinia ruckeri
A gene of an organism of Campylobacter jejuni subsp. jejuni
Bin Zhao, Oliver He
32022
gene of Campylobacter jejuni subsp. jejuni
A gene of an organism of Opisthokonta
Bin Zhao, Oliver He
33154
gene of Opisthokonta
A gene of an organism of Onygenales
Bin Zhao, Oliver He
33183
gene of Onygenales
A gene of an organism of Bilateria
Bin Zhao, Oliver He
33213
gene of Bilateria
A gene of an organism of Suid herpesvirus 1 strain Kaplan
Bin Zhao, Oliver He
33703
gene of Suid herpesvirus 1 strain Kaplan
A gene of an organism of Actinobacillus pleuropneumoniae serovar 2
Bin Zhao, Oliver He
34063
gene of Actinobacillus pleuropneumoniae serovar 2
A gene of an organism of dsDNA viruses, no RNA stage
Bin Zhao, Oliver He
35237
gene of dsDNA viruses, no RNA stage
A gene of an organism of Bovine herpesvirus 5
Bin Zhao, Oliver He
35244
gene of Bovine herpesvirus 5
A gene of an organism of ssRNA positive-strand viruses, no DNA stage
Bin Zhao, Oliver He
35278
gene of ssRNA positive-strand viruses, no DNA stage
A gene of an organism of ssRNA negative-strand viruses
Bin Zhao, Oliver He
35301
gene of ssRNA negative-strand viruses
A gene of an organism of Dictyochales
Bin Zhao, Oliver He
35685
gene of Dictyochales
A gene of an organism of Plasmodium falciparum 3D7
Bin Zhao, Oliver He
36329
gene of Plasmodium falciparum 3D7
A gene of an organism of Rotavirus C
Bin Zhao, Oliver He
36427
gene of Rotavirus C
A gene of an organism of Clostridium botulinum A
Bin Zhao, Oliver He
36826
gene of Clostridium botulinum A
A gene of an organism of Bartonella henselae
Bin Zhao, Oliver He
38323
gene of Bartonella henselae
A gene of an organism of Leishmania <subgenus>
Bin Zhao, Oliver He
38568
gene of Leishmania <subgenus>
A gene of an organism of Leishmania donovani species complex
Bin Zhao, Oliver He
38574
gene of Leishmania donovani species complex
A gene of an organism of Circoviridae
Bin Zhao, Oliver He
39724
gene of Circoviridae
A gene of an organism of Cryptococcus neoformans var. neoformans
Bin Zhao, Oliver He
40410
gene of Cryptococcus neoformans var. neoformans
A gene of an organism of Candida dubliniensis
Bin Zhao, Oliver He
42374
gene of Candida dubliniensis
A gene of an organism of Shigella flexneri 2a
Bin Zhao, Oliver He
42897
gene of Shigella flexneri 2a
A gene of an organism of Vibrio cholerae O139
Bin Zhao, Oliver He
45888
gene of Vibrio cholerae O139
A gene of an organism of Autographa californica nucleopolyhedrovirus
Bin Zhao, Oliver He
46015
gene of Autographa californica nucleopolyhedrovirus
A gene of an organism of Staphylococcus aureus subsp. aureus
Bin Zhao, Oliver He
46170
gene of Staphylococcus aureus subsp. aureus
A gene of an organism of Salmonella enterica subsp. enterica
Bin Zhao, Oliver He
59201
gene of Salmonella enterica subsp. enterica
A gene of an organism of Legionella pneumophila serogroup 1
Bin Zhao, Oliver He
66976
gene of Legionella pneumophila serogroup 1
A gene of an organism of Murine cytomegalovirus (strain K181)
Bin Zhao, Oliver He
69156
gene of Murine cytomegalovirus (strain K181)
A gene of an organism of Haemophilus influenzae Rd KW20
Bin Zhao, Oliver He
71421
gene of Haemophilus influenzae Rd KW20
A gene of an organism of Plasmodium yoelii yoelii
Bin Zhao, Oliver He
73239
gene of Plasmodium yoelii yoelii
A gene of an organism of Mannheimia haemolytica
Bin Zhao, Oliver He
75985
gene of Mannheimia haemolytica
A gene of an organism of Nidovirales
Bin Zhao, Oliver He
76804
gene of Nidovirales
A gene of an organism of Bovine herpesvirus type 1.1
Bin Zhao, Oliver He
79889
gene of Bovine herpesvirus type 1.1
A gene of an organism of Burkholderiales
Bin Zhao, Oliver He
80840
gene of Burkholderiales
A gene of an organism of Mycobacterium tuberculosis CDC1551
Bin Zhao, Oliver He
83331
gene of Mycobacterium tuberculosis CDC1551
A gene of an organism of Mycobacterium tuberculosis H37Rv
Bin Zhao, Oliver He
83332
gene of Mycobacterium tuberculosis H37Rv
A gene of an organism of Escherichia coli K-12
Bin Zhao, Oliver He
83333
gene of Escherichia coli K-12
A gene of an organism of Escherichia coli O157:H7
Bin Zhao, Oliver He
83334
gene of Escherichia coli O157:H7
A gene of an organism of Chlamydia pneumoniae
Bin Zhao, Oliver He
83558
gene of Chlamydia pneumoniae
A gene of an organism of Corynebacterineae
Bin Zhao, Oliver He
85007
gene of Corynebacterineae
A gene of an organism of Porcine circovirus 2
Bin Zhao, Oliver He
85708
gene of Porcine circovirus 2
A gene of an organism of Helicobacter pylori 26695
Bin Zhao, Oliver He
85962
gene of Helicobacter pylori 26695
A gene of an organism of Helicobacter pylori J99
Bin Zhao, Oliver He
85963
gene of Helicobacter pylori J99
A gene of an organism of Salmonella enterica subsp. enterica serovar Typhi
Bin Zhao, Oliver He
90370
gene of Salmonella enterica subsp. enterica serovar Typhi
A gene of an organism of Salmonella enterica subsp. enterica serovar Typhimurium
Bin Zhao, Oliver He
90371
gene of Salmonella enterica subsp. enterica serovar Typhimurium
A gene of an organism of Bacilli
Bin Zhao, Oliver He
91061
gene of Bacilli
A gene of an organism of Staphylococcus aureus subsp. aureus NCTC 8325
Bin Zhao, Oliver He
93061
gene of Staphylococcus aureus subsp. aureus NCTC 8325
A gene of an organism of Influenza A virus (A/Goose/Guangdong/1/96(H5N1))
Bin Zhao, Oliver He
93838
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
Bin Zhao, Oliver He
99287
gene of Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
A gene of an organism of H5N1 subtype
Bin Zhao, Oliver He
102793
gene of H5N1 subtype
A gene of an organism of Bartonella birtlesii
Bin Zhao, Oliver He
111504
gene of Bartonella birtlesii
A gene of an organism of pseudomallei group
Bin Zhao, Oliver He
111527
gene of pseudomallei group
A gene of an organism of Chlamydophila pneumoniae CWL029
Bin Zhao, Oliver He
115713
gene of Chlamydophila pneumoniae CWL029
A gene of an organism of Legionellales
Bin Zhao, Oliver He
118969
gene of Legionellales
A gene of an organism of Francisella tularensis subsp. holarctica
Bin Zhao, Oliver He
119857
gene of Francisella tularensis subsp. holarctica
A gene of an organism of Nipah virus
Bin Zhao, Oliver He
121791
gene of Nipah virus
A gene of an organism of Neisseria meningitidis MC58
Bin Zhao, Oliver He
122586
gene of Neisseria meningitidis MC58
A gene of an organism of Neisseria meningitidis Z2491
Bin Zhao, Oliver He
122587
gene of Neisseria meningitidis Z2491
A gene of an organism of Neisseria meningitidis serogroup C
Bin Zhao, Oliver He
135720
gene of Neisseria meningitidis serogroup C
A gene of an organism of Chlamydophila pneumoniae J138
Bin Zhao, Oliver He
138677
gene of Chlamydophila pneumoniae J138
A gene of an organism of Eurotiomycetes
Bin Zhao, Oliver He
147545
gene of Eurotiomycetes
A gene of an organism of Escherichia coli O157:H7 str. EDL933
Bin Zhao, Oliver He
155864
gene of Escherichia coli O157:H7 str. EDL933
A gene of an organism of Staphylococcus aureus subsp. aureus Mu50
Bin Zhao, Oliver He
158878
gene of Staphylococcus aureus subsp. aureus Mu50
A gene of an organism of Staphylococcus aureus subsp. aureus N315
Bin Zhao, Oliver He
158879
gene of Staphylococcus aureus subsp. aureus N315
A gene of an organism of Streptococcus pyogenes M1 GAS
Bin Zhao, Oliver He
160490
gene of Streptococcus pyogenes M1 GAS
A gene of an organism of Streptococcus pyogenes str. Manfredo
Bin Zhao, Oliver He
160491
gene of Streptococcus pyogenes str. Manfredo
A gene of an organism of Emericella nidulans
Bin Zhao, Oliver He
162425
gene of Emericella nidulans
A gene of an organism of Listeria monocytogenes EGD-e
Bin Zhao, Oliver He
169963
gene of Listeria monocytogenes EGD-e
A gene of an organism of Streptococcus pneumoniae TIGR4
Bin Zhao, Oliver He
170187
gene of Streptococcus pneumoniae TIGR4
A gene of an organism of Streptococcus pneumoniae R6
Bin Zhao, Oliver He
171101
gene of Streptococcus pneumoniae R6
A gene of an organism of Francisella tularensis subsp. tularensis SCHU S4
Bin Zhao, Oliver He
177416
gene of Francisella tularensis subsp. tularensis SCHU S4
A gene of an organism of WEEV complex
Bin Zhao, Oliver He
177874
gene of WEEV complex
A gene of an organism of Cryptococcus neoformans var. grubii
Bin Zhao, Oliver He
178876
gene of Cryptococcus neoformans var. grubii
A gene of an organism of Chlamydophila pneumoniae TW-183
Bin Zhao, Oliver He
182082
gene of Chlamydophila pneumoniae TW-183
A gene of an organism of Trypanosoma brucei TREU927
Bin Zhao, Oliver He
185431
gene of Trypanosoma brucei TREU927
A gene of an organism of Streptococcus pyogenes MGAS8232
Bin Zhao, Oliver He
186103
gene of Streptococcus pyogenes MGAS8232
A gene of an organism of Zaire ebolavirus
Bin Zhao, Oliver He
186538
gene of Zaire ebolavirus
A gene of an organism of Clostridiales
Bin Zhao, Oliver He
186802
gene of Clostridiales
A gene of an organism of Lactobacillales
Bin Zhao, Oliver He
186826
gene of Lactobacillales
A gene of an organism of Yersinia pestis KIM10+
Bin Zhao, Oliver He
187410
gene of Yersinia pestis KIM10+
A gene of an organism of Leptospira interrogans serovar Lai str. 56601
Bin Zhao, Oliver He
189518
gene of Leptospira interrogans serovar Lai str. 56601
A gene of an organism of Bacillus anthracis str. A2012
Bin Zhao, Oliver He
191218
gene of Bacillus anthracis str. A2012
A gene of an organism of Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
Bin Zhao, Oliver He
192222
gene of Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
A gene of an organism of Streptococcus pyogenes SSI-1
Bin Zhao, Oliver He
193567
gene of Streptococcus pyogenes SSI-1
A gene of an organism of Campylobacter jejuni RM1221
Bin Zhao, Oliver He
195099
gene of Campylobacter jejuni RM1221
A gene of an organism of Clostridium perfringens str. 13
Bin Zhao, Oliver He
195102
gene of Clostridium perfringens str. 13
A gene of an organism of Clostridium perfringens ATCC 13124
Bin Zhao, Oliver He
195103
gene of Clostridium perfringens ATCC 13124
A gene of an organism of Staphylococcus aureus subsp. aureus MW2
Bin Zhao, Oliver He
196620
gene of Staphylococcus aureus subsp. aureus MW2
A gene of an organism of Bacillus anthracis str. Ames
Bin Zhao, Oliver He
198094
gene of Bacillus anthracis str. Ames
A gene of an organism of Shigella flexneri 2a str. 301
Bin Zhao, Oliver He
198214
gene of Shigella flexneri 2a str. 301
A gene of an organism of Shigella flexneri 2a str. 2457T
Bin Zhao, Oliver He
198215
gene of Shigella flexneri 2a str. 2457T
A gene of an organism of Streptococcus pyogenes MGAS315
Bin Zhao, Oliver He
198466
gene of Streptococcus pyogenes MGAS315
A gene of an organism of Coccidioides posadasii
Bin Zhao, Oliver He
199306
gene of Coccidioides posadasii
A gene of an organism of Escherichia coli CFT073
Bin Zhao, Oliver He
199310
gene of Escherichia coli CFT073
A gene of an organism of Brucella suis 1330
Bin Zhao, Oliver He
204722
gene of Brucella suis 1330
A gene of an organism of Streptococcus agalactiae A909
Bin Zhao, Oliver He
205921
gene of Streptococcus agalactiae A909
A gene of an organism of Streptococcus agalactiae 2603V/R
Bin Zhao, Oliver He
208435
gene of Streptococcus agalactiae 2603V/R
A gene of an organism of Pseudomonas aeruginosa UCBPP-PA14
Bin Zhao, Oliver He
208963
gene of Pseudomonas aeruginosa UCBPP-PA14
A gene of an organism of Pseudomonas aeruginosa PAO1
Bin Zhao, Oliver He
208964
gene of Pseudomonas aeruginosa PAO1
A gene of an organism of Salmonella enterica subsp. enterica serovar Typhi str. Ty2
Bin Zhao, Oliver He
209261
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))
Bin Zhao, Oliver He
211044
gene of Influenza A virus (A/Puerto Rico/8/1934(H1N1))
A gene of an organism of Streptococcus agalactiae NEM316
Bin Zhao, Oliver He
211110
gene of Streptococcus agalactiae NEM316
A gene of an organism of Clostridium tetani E88
Bin Zhao, Oliver He
212717
gene of Clostridium tetani E88
A gene of an organism of Campylobacterales
Bin Zhao, Oliver He
213849
gene of Campylobacterales
A gene of an organism of Yersinia pestis CO92
Bin Zhao, Oliver He
214092
gene of Yersinia pestis CO92
A gene of an organism of Cryptococcus neoformans var. neoformans JEC21
Bin Zhao, Oliver He
214684
gene of Cryptococcus neoformans var. neoformans JEC21
A gene of an organism of Salmonella enterica subsp. enterica serovar Typhi str. CT18
Bin Zhao, Oliver He
220341
gene of Salmonella enterica subsp. enterica serovar Typhi str. CT18
A gene of an organism of Borrelia burgdorferi B31
Bin Zhao, Oliver He
224326
gene of Borrelia burgdorferi B31
A gene of an organism of Brucella melitensis bv. 1 str. 16M
Bin Zhao, Oliver He
224914
gene of Brucella melitensis bv. 1 str. 16M
A gene of an organism of Enterococcus faecalis V583
Bin Zhao, Oliver He
226185
gene of Enterococcus faecalis V583
A gene of an organism of Aspergillus nidulans FGSC A4
Bin Zhao, Oliver He
227321
gene of Aspergillus nidulans FGSC A4
A gene of an organism of Coxiella burnetii RSA 493
Bin Zhao, Oliver He
227377
gene of Coxiella burnetii RSA 493
A gene of an organism of Yersinia pestis biovar Microtus str. 91001
Bin Zhao, Oliver He
229193
gene of Yersinia pestis biovar Microtus str. 91001
A gene of an organism of Candida albicans SC5314
Bin Zhao, Oliver He
237561
gene of Candida albicans SC5314
A gene of an organism of Burkholderia mallei ATCC 23344
Bin Zhao, Oliver He
243160
gene of Burkholderia mallei ATCC 23344
A gene of an organism of Vibrio cholerae O1 biovar El Tor str. N16961
Bin Zhao, Oliver He
243277
gene of Vibrio cholerae O1 biovar El Tor str. N16961
A gene of an organism of Corynebacterium diphtheriae NCTC 13129
Bin Zhao, Oliver He
257309
gene of Corynebacterium diphtheriae NCTC 13129
A gene of an organism of Bordetella bronchiseptica RB50
Bin Zhao, Oliver He
257310
gene of Bordetella bronchiseptica RB50
A gene of an organism of Bordetella pertussis Tohama I
Bin Zhao, Oliver He
257313
gene of Bordetella pertussis Tohama I
A gene of an organism of Bacillus anthracis str. Sterne
Bin Zhao, Oliver He
260799
gene of Bacillus anthracis str. Sterne
A gene of an organism of Bacillus anthracis str. 'Ames Ancestor'
Bin Zhao, Oliver He
261594
gene of Bacillus anthracis str. 'Ames Ancestor'
A gene of an organism of Orgyia pseudotsugata MNPV
Bin Zhao, Oliver He
262177
gene of Orgyia pseudotsugata MNPV
A gene of an organism of Mycobacterium avium subsp. paratuberculosis K-10
Bin Zhao, Oliver He
262316
gene of Mycobacterium avium subsp. paratuberculosis K-10
A gene of an organism of Listeria monocytogenes serotype 4b str. F2365
Bin Zhao, Oliver He
265669
gene of Listeria monocytogenes serotype 4b str. F2365
A gene of an organism of Pneumonia virus of mice J3666
Bin Zhao, Oliver He
270473
gene of Pneumonia virus of mice J3666
A gene of an organism of Bombyx mori NPV
Bin Zhao, Oliver He
271108
gene of Bombyx mori NPV
A gene of an organism of Burkholderia pseudomallei K96243
Bin Zhao, Oliver He
272560
gene of Burkholderia pseudomallei K96243
A gene of an organism of Chlamydia trachomatis D/UW-3/CX
Bin Zhao, Oliver He
272561
gene of Chlamydia trachomatis D/UW-3/CX
A gene of an organism of Clostridium difficile 630
Bin Zhao, Oliver He
272563
gene of Clostridium difficile 630
A gene of an organism of Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Bin Zhao, Oliver He
272624
gene of Legionella pneumophila subsp. pneumophila str. Philadelphia 1
A gene of an organism of Neisseria meningitidis FAM18
Bin Zhao, Oliver He
272831
gene of Neisseria meningitidis FAM18
A gene of an organism of Pasteurella multocida subsp. multocida str. Pm70
Bin Zhao, Oliver He
272843
gene of Pasteurella multocida subsp. multocida str. Pm70
A gene of an organism of Rickettsia prowazekii str. Madrid E
Bin Zhao, Oliver He
272947
gene of Rickettsia prowazekii str. Madrid E
A gene of an organism of Staphylococcus aureus RF122
Bin Zhao, Oliver He
273036
gene of Staphylococcus aureus RF122
A gene of an organism of Yersinia pseudotuberculosis IP 32953
Bin Zhao, Oliver He
273123
gene of Yersinia pseudotuberculosis IP 32953
A gene of an organism of Haemophilus influenzae 86-028NP
Bin Zhao, Oliver He
281310
gene of Haemophilus influenzae 86-028NP
A gene of an organism of Staphylococcus aureus subsp. aureus MRSA252
Bin Zhao, Oliver He
282458
gene of Staphylococcus aureus subsp. aureus MRSA252
A gene of an organism of Bartonella henselae str. Houston-1
Bin Zhao, Oliver He
283166
gene of Bartonella henselae str. Houston-1
A gene of an organism of Cryptococcus neoformans var. neoformans B-3501A
Bin Zhao, Oliver He
283643
gene of Cryptococcus neoformans var. neoformans B-3501A
A gene of an organism of Influenza A virus (A/Viet Nam/1203/2004(H5N1))
Bin Zhao, Oliver He
284218
gene of Influenza A virus (A/Viet Nam/1203/2004(H5N1))
A gene of an organism of Candida glabrata CBS 138
Bin Zhao, Oliver He
284593
gene of Candida glabrata CBS 138
A gene of an organism of Streptococcus pyogenes MGAS10394
Bin Zhao, Oliver He
286636
gene of Streptococcus pyogenes MGAS10394
A gene of an organism of Clostridium perfringens SM101
Bin Zhao, Oliver He
289380
gene of Clostridium perfringens SM101
A gene of an organism of Streptococcus pyogenes MGAS5005
Bin Zhao, Oliver He
293653
gene of Streptococcus pyogenes MGAS5005
A gene of an organism of Entamoeba histolytica HM-1:IMSS
Bin Zhao, Oliver He
294381
gene of Entamoeba histolytica HM-1:IMSS
A gene of an organism of Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
Bin Zhao, Oliver He
295319
gene of Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
A gene of an organism of Legionella pneumophila str. Lens
Bin Zhao, Oliver He
297245
gene of Legionella pneumophila str. Lens
A gene of an organism of Legionella pneumophila str. Paris
Bin Zhao, Oliver He
297246
gene of Legionella pneumophila str. Paris
A gene of an organism of Shigella dysenteriae Sd197
Bin Zhao, Oliver He
300267
gene of Shigella dysenteriae Sd197
A gene of an organism of Shigella boydii Sb227
Bin Zhao, Oliver He
300268
gene of Shigella boydii Sb227
A gene of an organism of Shigella sonnei Ss046
Bin Zhao, Oliver He
300269
gene of Shigella sonnei Ss046
A gene of an organism of Streptococcus pyogenes serotype M1
Bin Zhao, Oliver He
301447
gene of Streptococcus pyogenes serotype M1
A gene of an organism of Streptococcus pyogenes serotype M3
Bin Zhao, Oliver He
301448
gene of Streptococcus pyogenes serotype M3
A gene of an organism of Escherichia coli str. K-12 substr. DH10B
Bin Zhao, Oliver He
316385
gene of Escherichia coli str. K-12 substr. DH10B
A gene of an organism of Escherichia coli ETEC H10407
Bin Zhao, Oliver He
316401
gene of Escherichia coli ETEC H10407
A gene of an organism of Streptococcus pyogenes MGAS6180
Bin Zhao, Oliver He
319701
gene of Streptococcus pyogenes MGAS6180
A gene of an organism of Burkholderia pseudomallei 1710b
Bin Zhao, Oliver He
320372
gene of Burkholderia pseudomallei 1710b
A gene of an organism of Burkholderia pseudomallei 668
Bin Zhao, Oliver He
320373
gene of Burkholderia pseudomallei 668
A gene of an organism of Burkholderia mallei SAVP1
Bin Zhao, Oliver He
320388
gene of Burkholderia mallei SAVP1
A gene of an organism of Burkholderia mallei NCTC 10247
Bin Zhao, Oliver He
320389
gene of Burkholderia mallei NCTC 10247
A gene of an organism of Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
Bin Zhao, Oliver He
321314
gene of Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
A gene of an organism of Aspergillus fumigatus Af293
Bin Zhao, Oliver He
330879
gene of Aspergillus fumigatus Af293
A gene of an organism of Escherichia coli E24377A
Bin Zhao, Oliver He
331111
gene of Escherichia coli E24377A
A gene of an organism of Escherichia coli HS
Bin Zhao, Oliver He
331112
gene of Escherichia coli HS
A gene of an organism of Mycobacterium tuberculosis F11
Bin Zhao, Oliver He
336982
gene of Mycobacterium tuberculosis F11
A gene of an organism of Streptococcus pyogenes serotype M12
Bin Zhao, Oliver He
342023
gene of Streptococcus pyogenes serotype M12
A gene of an organism of Shigella boydii CDC 3083-94
Bin Zhao, Oliver He
344609
gene of Shigella boydii CDC 3083-94
A gene of an organism of SARS coronavirus ZJ0301
Bin Zhao, Oliver He
344702
gene of SARS coronavirus ZJ0301
A gene of an organism of Vibrio cholerae O395
Bin Zhao, Oliver He
345073
gene of Vibrio cholerae O395
A gene of an organism of Leishmania major strain Friedlin
Bin Zhao, Oliver He
347515
gene of Leishmania major strain Friedlin
A gene of an organism of Yersinia pestis Angola
Bin Zhao, Oliver He
349746
gene of Yersinia pestis Angola
A gene of an organism of Yersinia pseudotuberculosis IP 31758
Bin Zhao, Oliver He
349747
gene of Yersinia pseudotuberculosis IP 31758
A gene of an organism of Plasmodium yoelii yoelii 17XNL
Bin Zhao, Oliver He
352914
gene of Plasmodium yoelii yoelii 17XNL
A gene of an organism of Cryptosporidium parvum Iowa II
Bin Zhao, Oliver He
353152
gene of Cryptosporidium parvum Iowa II
A gene of an organism of Trypanosoma cruzi strain CL Brener
Bin Zhao, Oliver He
353153
gene of Trypanosoma cruzi strain CL Brener
A gene of an organism of Campylobacter jejuni subsp. jejuni 81-176
Bin Zhao, Oliver He
354242
gene of Campylobacter jejuni subsp. jejuni 81-176
A gene of an organism of Burkholderia pseudomallei 1106a
Bin Zhao, Oliver He
357348
gene of Burkholderia pseudomallei 1106a
A gene of an organism of Brucella melitensis biovar Abortus 2308
Bin Zhao, Oliver He
359391
gene of Brucella melitensis biovar Abortus 2308
A gene of an organism of Bartonella bacilliformis KC583
Bin Zhao, Oliver He
360095
gene of Bartonella bacilliformis KC583
A gene of an organism of Yersinia pestis Antiqua
Bin Zhao, Oliver He
360102
gene of Yersinia pestis Antiqua
A gene of an organism of Campylobacter jejuni subsp. doylei 269.97
Bin Zhao, Oliver He
360109
gene of Campylobacter jejuni subsp. doylei 269.97
A gene of an organism of Bordetella avium 197N
Bin Zhao, Oliver He
360910
gene of Bordetella avium 197N
A gene of an organism of Escherichia coli 536
Bin Zhao, Oliver He
362663
gene of Escherichia coli 536
A gene of an organism of Escherichia coli UTI89
Bin Zhao, Oliver He
364106
gene of Escherichia coli UTI89
A gene of an organism of Streptococcus pyogenes MGAS9429
Bin Zhao, Oliver He
370551
gene of Streptococcus pyogenes MGAS9429
A gene of an organism of Streptococcus pyogenes MGAS10270
Bin Zhao, Oliver He
370552
gene of Streptococcus pyogenes MGAS10270
A gene of an organism of Streptococcus pyogenes MGAS2096
Bin Zhao, Oliver He
370553
gene of Streptococcus pyogenes MGAS2096
A gene of an organism of Streptococcus pyogenes MGAS10750
Bin Zhao, Oliver He
370554
gene of Streptococcus pyogenes MGAS10750
A gene of an organism of Streptococcus pneumoniae D39
Bin Zhao, Oliver He
373153
gene of Streptococcus pneumoniae D39
A gene of an organism of Shigella flexneri 5 str. 8401
Bin Zhao, Oliver He
373384
gene of Shigella flexneri 5 str. 8401
A gene of an organism of Neisseria meningitidis 053442
Bin Zhao, Oliver He
374833
gene of Neisseria meningitidis 053442
A gene of an organism of Francisella tularensis subsp. holarctica LVS
Bin Zhao, Oliver He
376619
gene of Francisella tularensis subsp. holarctica LVS
A gene of an organism of Escherichia coli O26:H-
Bin Zhao, Oliver He
376724
gene of Escherichia coli O26:H-
A gene of an organism of Yersinia pestis Nepal516
Bin Zhao, Oliver He
377628
gene of Yersinia pestis Nepal516
A gene of an organism of Aeromonas salmonicida subsp. salmonicida A449
Bin Zhao, Oliver He
382245
gene of Aeromonas salmonicida subsp. salmonicida A449
A gene of an organism of Bartonella tribocorum CIP 105476
Bin Zhao, Oliver He
382640
gene of Bartonella tribocorum CIP 105476
A gene of an organism of Escherichia coli O157:H7 str. Sakai
Bin Zhao, Oliver He
386585
gene of Escherichia coli O157:H7 str. Sakai
A gene of an organism of Yersinia pestis Pestoides F
Bin Zhao, Oliver He
386656
gene of Yersinia pestis Pestoides F
A gene of an organism of Yersinia enterocolitica subsp. enterocolitica 8081
Bin Zhao, Oliver He
393305
gene of Yersinia enterocolitica subsp. enterocolitica 8081
A gene of an organism of Legionella pneumophila str. Corby
Bin Zhao, Oliver He
400673
gene of Legionella pneumophila str. Corby
A gene of an organism of Escherichia coli APEC O1
Bin Zhao, Oliver He
405955
gene of Escherichia coli APEC O1
A gene of an organism of Campylobacter jejuni subsp. jejuni 81116
Bin Zhao, Oliver He
407148
gene of Campylobacter jejuni subsp. jejuni 81116
A gene of an organism of Escherichia coli SE11
Bin Zhao, Oliver He
409438
gene of Escherichia coli SE11
A gene of an organism of Burkholderia mallei NCTC 10229
Bin Zhao, Oliver He
412022
gene of Burkholderia mallei NCTC 10229
A gene of an organism of Yersinia pestis CA88-4125
Bin Zhao, Oliver He
412420
gene of Yersinia pestis CA88-4125
A gene of an organism of Escherichia coli B str. REL606
Bin Zhao, Oliver He
413997
gene of Escherichia coli B str. REL606
A gene of an organism of Actinobacillus pleuropneumoniae serovar 5b str. L20
Bin Zhao, Oliver He
416269
gene of Actinobacillus pleuropneumoniae serovar 5b str. L20
A gene of an organism of Plasmodium (Vinckeia)
Bin Zhao, Oliver He
418101
gene of Plasmodium (Vinckeia)
A gene of an organism of Staphylococcus aureus subsp. aureus Mu3
Bin Zhao, Oliver He
418127
gene of Staphylococcus aureus subsp. aureus Mu3
A gene of an organism of Mycobacterium tuberculosis H37Ra
Bin Zhao, Oliver He
419947
gene of Mycobacterium tuberculosis H37Ra
A gene of an organism of Eimeriorina
Bin Zhao, Oliver He
423054
gene of Eimeriorina
A gene of an organism of Legionella pneumophila 2300/99 Alcoy
Bin Zhao, Oliver He
423212
gene of Legionella pneumophila 2300/99 Alcoy
A gene of an organism of Staphylococcus aureus subsp. aureus str. Newman
Bin Zhao, Oliver He
426430
gene of Staphylococcus aureus subsp. aureus str. Newman
A gene of an organism of Actinobacillus pleuropneumoniae serovar 3 str. JL03
Bin Zhao, Oliver He
434271
gene of Actinobacillus pleuropneumoniae serovar 3 str. JL03
A gene of an organism of ssRNA viruses
Bin Zhao, Oliver He
439488
gene of ssRNA viruses
A gene of an organism of Escherichia coli SMS-3-5
Bin Zhao, Oliver He
439855
gene of Escherichia coli SMS-3-5
A gene of an organism of Clostridium botulinum A str. ATCC 19397
Bin Zhao, Oliver He
441770
gene of Clostridium botulinum A str. ATCC 19397
A gene of an organism of Clostridium botulinum A str. Hall
Bin Zhao, Oliver He
441771
gene of Clostridium botulinum A str. Hall
A gene of an organism of Escherichia coli O157:H7 str. EC4115
Bin Zhao, Oliver He
444450
gene of Escherichia coli O157:H7 str. EC4115
A gene of an organism of Borrelia burgdorferi 156a
Bin Zhao, Oliver He
445983
gene of Borrelia burgdorferi 156a
A gene of an organism of Borrelia burgdorferi ZS7
Bin Zhao, Oliver He
445985
gene of Borrelia burgdorferi ZS7
A gene of an organism of Dikarya
Bin Zhao, Oliver He
451864
gene of Dikarya
A gene of an organism of Eurotiomycetidae
Bin Zhao, Oliver He
451871
gene of Eurotiomycetidae
A gene of an organism of Francisella tularensis subsp. holarctica FTNF002-00
Bin Zhao, Oliver He
458234
gene of Francisella tularensis subsp. holarctica FTNF002-00
A gene of an organism of Streptococcus pyogenes NZ131
Bin Zhao, Oliver He
471876
gene of Streptococcus pyogenes NZ131
A gene of an organism of Enterococcus faecalis OG1RF
Bin Zhao, Oliver He
474186
gene of Enterococcus faecalis OG1RF
A gene of an organism of Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
Bin Zhao, Oliver He
476213
gene of Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
A gene of an organism of Paenibacillus sp. Y412MC10
Bin Zhao, Oliver He
481743
gene of Paenibacillus sp. Y412MC10
A gene of an organism of Streptococcus pneumoniae Taiwan19F-14
Bin Zhao, Oliver He
487213
gene of Streptococcus pneumoniae Taiwan19F-14
A gene of an organism of Streptococcus pneumoniae Hungary19A-6
Bin Zhao, Oliver He
487214
gene of Streptococcus pneumoniae Hungary19A-6
A gene of an organism of Streptococcus pneumoniae 70585
Bin Zhao, Oliver He
488221
gene of Streptococcus pneumoniae 70585
A gene of an organism of Streptococcus pneumoniae JJA
Bin Zhao, Oliver He
488222
gene of Streptococcus pneumoniae JJA
A gene of an organism of Streptococcus pneumoniae P1031
Bin Zhao, Oliver He
488223
gene of Streptococcus pneumoniae P1031
A gene of an organism of Clostridium botulinum B1 str. Okra
Bin Zhao, Oliver He
498213
gene of Clostridium botulinum B1 str. Okra
A gene of an organism of Clostridium botulinum A3 str. Loch Maree
Bin Zhao, Oliver He
498214
gene of Clostridium botulinum A3 str. Loch Maree
A gene of an organism of Edwardsiella tarda EIB202
Bin Zhao, Oliver He
498217
gene of Edwardsiella tarda EIB202
A gene of an organism of Yersinia pseudotuberculosis YPIII
Bin Zhao, Oliver He
502800
gene of Yersinia pseudotuberculosis YPIII
A gene of an organism of Yersinia pseudotuberculosis PB1/+
Bin Zhao, Oliver He
502801
gene of Yersinia pseudotuberculosis PB1/+
A gene of an organism of Clostridium botulinum E3 str. Alaska E43
Bin Zhao, Oliver He
508767
gene of Clostridium botulinum E3 str. Alaska E43
A gene of an organism of Toxoplasma gondii ME49
Bin Zhao, Oliver He
508771
gene of Toxoplasma gondii ME49
A gene of an organism of Escherichia coli str. K-12 substr. MG1655
Bin Zhao, Oliver He
511145
gene of Escherichia coli str. K-12 substr. MG1655
A gene of an organism of Streptococcus pneumoniae G54
Bin Zhao, Oliver He
512566
gene of Streptococcus pneumoniae G54
A gene of an organism of Streptococcus pneumoniae CGSP14
Bin Zhao, Oliver He
516950
gene of Streptococcus pneumoniae CGSP14
A gene of an organism of Borrelia burgdorferi N40
Bin Zhao, Oliver He
521007
gene of Borrelia burgdorferi N40
A gene of an organism of Borrelia burgdorferi 297
Bin Zhao, Oliver He
521009
gene of Borrelia burgdorferi 297
A gene of an organism of Burkholderia pseudomallei MSHR346
Bin Zhao, Oliver He
536230
gene of Burkholderia pseudomallei MSHR346
A gene of an organism of Actinobacillus pleuropneumoniae serovar 7 str. AP76
Bin Zhao, Oliver He
537457
gene of Actinobacillus pleuropneumoniae serovar 7 str. AP76
A gene of an organism of Escherichia coli O157:H7 str. TW14359
Bin Zhao, Oliver He
544404
gene of Escherichia coli O157:H7 str. TW14359
A gene of an organism of Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
Bin Zhao, Oliver He
550537
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
Bin Zhao, Oliver He
550538
gene of Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91
A gene of an organism of Filobasidiella/Cryptococcus neoformans species complex
Bin Zhao, Oliver He
552466
gene of Filobasidiella/Cryptococcus neoformans species complex
A gene of an organism of Cryptococcus gattii
Bin Zhao, Oliver He
552467
gene of Cryptococcus gattii
A gene of an organism of Streptococcus equi subsp. zooepidemicus MGCS10565
Bin Zhao, Oliver He
552526
gene of Streptococcus equi subsp. zooepidemicus MGCS10565
A gene of an organism of Listeria monocytogenes HCC23
Bin Zhao, Oliver He
552536
gene of Listeria monocytogenes HCC23
A gene of an organism of Pseudomonas aeruginosa LESB58
Bin Zhao, Oliver He
557722
gene of Pseudomonas aeruginosa LESB58
A gene of an organism of Alphabaculovirus
Bin Zhao, Oliver He
558016
gene of Alphabaculovirus
A gene of an organism of Saccharomyces cerevisiae S288c
Bin Zhao, Oliver He
559292
gene of Saccharomyces cerevisiae S288c
A gene of an organism of Streptococcus pneumoniae ATCC 700669
Bin Zhao, Oliver He
561276
gene of Streptococcus pneumoniae ATCC 700669
A gene of an organism of Helicobacter pylori G27
Bin Zhao, Oliver He
563041
gene of Helicobacter pylori G27
A gene of an organism of Listeria monocytogenes L99
Bin Zhao, Oliver He
563174
gene of Listeria monocytogenes L99
A gene of an organism of Escherichia coli Vir68
Bin Zhao, Oliver He
563770
gene of Escherichia coli Vir68
A gene of an organism of Bacillus anthracis str. CDC 684
Bin Zhao, Oliver He
568206
gene of Bacillus anthracis str. CDC 684
A gene of an organism of Listeria monocytogenes serotype 4b str. CLIP 80459
Bin Zhao, Oliver He
568819
gene of Listeria monocytogenes serotype 4b str. CLIP 80459
A gene of an organism of Helicobacter pylori P12
Bin Zhao, Oliver He
570508
gene of Helicobacter pylori P12
A gene of an organism of Escherichia coli O26:H11 str. 11368
Bin Zhao, Oliver He
573235
gene of Escherichia coli O26:H11 str. 11368
A gene of an organism of Escherichia coli O127:H6 str. E2348/69
Bin Zhao, Oliver He
574521
gene of Escherichia coli O127:H6 str. E2348/69
A gene of an organism of Vibrio cholerae M66-2
Bin Zhao, Oliver He
579112
gene of Vibrio cholerae M66-2
A gene of an organism of Escherichia coli IAI1
Bin Zhao, Oliver He
585034
gene of Escherichia coli IAI1
A gene of an organism of Escherichia coli S88
Bin Zhao, Oliver He
585035
gene of Escherichia coli S88
A gene of an organism of Escherichia coli 55989
Bin Zhao, Oliver He
585055
gene of Escherichia coli 55989
A gene of an organism of Escherichia coli UMN026
Bin Zhao, Oliver He
585056
gene of Escherichia coli UMN026
A gene of an organism of Escherichia coli IAI39
Bin Zhao, Oliver He
585057
gene of Escherichia coli IAI39
A gene of an organism of Escherichia coli O103:H2 str. 12009
Bin Zhao, Oliver He
585395
gene of Escherichia coli O103:H2 str. 12009
A gene of an organism of Escherichia coli O111:H- str. 11128
Bin Zhao, Oliver He
585396
gene of Escherichia coli O111:H- str. 11128
A gene of an organism of Escherichia coli ED1a
Bin Zhao, Oliver He
585397
gene of Escherichia coli ED1a
A gene of an organism of Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
Bin Zhao, Oliver He
588858
gene of Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
A gene of an organism of Bacillus anthracis str. A0248
Bin Zhao, Oliver He
592021
gene of Bacillus anthracis str. A0248
A gene of an organism of Helicobacter pylori B38
Bin Zhao, Oliver He
592205
gene of Helicobacter pylori B38
A gene of an organism of Escherichia coli BW2952
Bin Zhao, Oliver He
595496
gene of Escherichia coli BW2952
A gene of an organism of SARS coronavirus ExoN1
Bin Zhao, Oliver He
627440
gene of SARS coronavirus ExoN1
A gene of an organism of Listeria monocytogenes 08-5923
Bin Zhao, Oliver He
637381
gene of Listeria monocytogenes 08-5923
A gene of an organism of Listeria monocytogenes 08-5578
Bin Zhao, Oliver He
653938
gene of Listeria monocytogenes 08-5578
A gene of an organism of Neisseria meningitidis alpha14
Bin Zhao, Oliver He
662598
gene of Neisseria meningitidis alpha14
A gene of an organism of Staphylococcus aureus subsp. aureus ED98
Bin Zhao, Oliver He
681288
gene of Staphylococcus aureus subsp. aureus ED98
A gene of an organism of Coronavirinae
Bin Zhao, Oliver He
693995
gene of Coronavirinae
A gene of an organism of Alphacoronavirus 1
Bin Zhao, Oliver He
693997
gene of Alphacoronavirus 1
A gene of an organism of Severe acute respiratory syndrome-related coronavirus
Bin Zhao, Oliver He
694009
gene of Severe acute respiratory syndrome-related coronavirus
A gene of an organism of Human metapneumovirus CAN97-83
Bin Zhao, Oliver He
694067
gene of Human metapneumovirus CAN97-83
A gene of an organism of Mileewa branchiuma
Bin Zhao, Oliver He
700720
gene of Mileewa branchiuma
A gene of an organism of Staphylococcus aureus 04-02981
Bin Zhao, Oliver He
703339
gene of Staphylococcus aureus 04-02981
A gene of an organism of Mycoplasma gallisepticum str. R(low)
Bin Zhao, Oliver He
710127
gene of Mycoplasma gallisepticum str. R(low)
A gene of an organism of saccharomyceta
Bin Zhao, Oliver He
716545
gene of saccharomyceta
A gene of an organism of Legionella pneumophila 130b
Bin Zhao, Oliver He
866628
gene of Legionella pneumophila 130b
A gene of an organism of Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74
Bin Zhao, Oliver He
909946
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
Bin Zhao, Oliver He
376619
tRNA gene of Francisella tularensis subsp. holarctica LVS
A gene of Francisella tularensis subsp. tularensis SCHU S4 that has a rRNA gene type
Bin Zhao, Oliver He
177416
rRNA gene of Francisella tularensis subsp. tularensis SCHU S4
A gene of Francisella tularensis subsp. holarctica LVS that has a rRNA gene type
Bin Zhao, Oliver He
376619
rRNA gene of Francisella tularensis subsp. holarctica LVS
A gene of Campylobacter jejuni that has a protein-coding gene type
Bin Zhao, Oliver He
197
protein-coding gene of Campylobacter jejuni
A gene of Escherichia coli that has a protein-coding gene type
Bin Zhao, Oliver He
562
protein-coding gene of Escherichia coli
A gene of Yersinia enterocolitica that has a protein-coding gene type
Bin Zhao, Oliver He
630
protein-coding gene of Yersinia enterocolitica
A gene of Yersinia pestis that has a protein-coding gene type
Bin Zhao, Oliver He
632
protein-coding gene of Yersinia pestis
A gene of Enterococcus faecalis that has a protein-coding gene type
Bin Zhao, Oliver He
1351
protein-coding gene of Enterococcus faecalis
A gene of Clostridium botulinum that has a protein-coding gene type
Bin Zhao, Oliver He
1491
protein-coding gene of Clostridium botulinum
A gene of Clostridium perfringens that has a protein-coding gene type
Bin Zhao, Oliver He
1502
protein-coding gene of Clostridium perfringens
A gene of Listeria monocytogenes that has a protein-coding gene type
Bin Zhao, Oliver He
1639
protein-coding gene of Listeria monocytogenes
A gene of Plasmodium berghei ANKA that has a protein-coding gene type
Bin Zhao, Oliver He
5823
protein-coding gene of Plasmodium berghei ANKA
A gene of Cowpox virus that has a protein-coding gene type
Bin Zhao, Oliver He
10243
protein-coding gene of Cowpox virus
A gene of Vaccinia virus that has a protein-coding gene type
Bin Zhao, Oliver He
10245
protein-coding gene of Vaccinia virus
A gene of Sheeppox virus that has a protein-coding gene type
Bin Zhao, Oliver He
10266
protein-coding gene of Sheeppox virus
A gene of Rabbit fibroma virus that has a protein-coding gene type
Bin Zhao, Oliver He
10271
protein-coding gene of Rabbit fibroma virus
A gene of Myxoma virus that has a protein-coding gene type
Bin Zhao, Oliver He
10273
protein-coding gene of Myxoma virus
A gene of Human herpesvirus 1 that has a protein-coding gene type
Bin Zhao, Oliver He
10298
protein-coding gene of Human herpesvirus 1
A gene of Human herpesvirus 2 that has a protein-coding gene type
Bin Zhao, Oliver He
10310
protein-coding gene of Human herpesvirus 2
A gene of Bovine herpesvirus 1 that has a protein-coding gene type
Bin Zhao, Oliver He
10320
protein-coding gene of Bovine herpesvirus 1
A gene of Felid herpesvirus 1 that has a protein-coding gene type
Bin Zhao, Oliver He
10334
protein-coding gene of Felid herpesvirus 1
A gene of Human herpesvirus 3 that has a protein-coding gene type
Bin Zhao, Oliver He
10335
protein-coding gene of Human herpesvirus 3
A gene of Suid herpesvirus 1 that has a protein-coding gene type
Bin Zhao, Oliver He
10345
protein-coding gene of Suid herpesvirus 1
A gene of Gallid herpesvirus 1 that has a protein-coding gene type
Bin Zhao, Oliver He
10386
protein-coding gene of Gallid herpesvirus 1
A gene of Gallid herpesvirus 2 that has a protein-coding gene type
Bin Zhao, Oliver He
10390
protein-coding gene of Gallid herpesvirus 2
A gene of African swine fever virus that has a protein-coding gene type
Bin Zhao, Oliver He
10497
protein-coding gene of African swine fever virus
A gene of Ross River virus that has a protein-coding gene type
Bin Zhao, Oliver He
11029
protein-coding gene of Ross River virus
A gene of Classical swine fever virus that has a protein-coding gene type
Bin Zhao, Oliver He
11096
protein-coding gene of Classical swine fever virus
A gene of Feline infectious peritonitis virus that has a protein-coding gene type
Bin Zhao, Oliver He
11135
protein-coding gene of Feline infectious peritonitis virus
A gene of Measles virus that has a protein-coding gene type
Bin Zhao, Oliver He
11234
protein-coding gene of Measles virus
A gene of Bovine respiratory syncytial virus that has a protein-coding gene type
Bin Zhao, Oliver He
11246
protein-coding gene of Bovine respiratory syncytial virus
A gene of Infectious hematopoietic necrosis virus that has a protein-coding gene type
Bin Zhao, Oliver He
11290
protein-coding gene of Infectious hematopoietic necrosis virus
A gene of Rabies virus that has a protein-coding gene type
Bin Zhao, Oliver He
11292
protein-coding gene of Rabies virus
A gene of La Crosse virus that has a protein-coding gene type
Bin Zhao, Oliver He
11577
protein-coding gene of La Crosse virus
A gene of Hantaan virus that has a protein-coding gene type
Bin Zhao, Oliver He
11599
protein-coding gene of Hantaan virus
A gene of Feline immunodeficiency virus that has a protein-coding gene type
Bin Zhao, Oliver He
11673
protein-coding gene of Feline immunodeficiency virus
A gene of Human immunodeficiency virus 1 that has a protein-coding gene type
Bin Zhao, Oliver He
11676
protein-coding gene of Human immunodeficiency virus 1
A gene of Simian immunodeficiency virus that has a protein-coding gene type
Bin Zhao, Oliver He
11723
protein-coding gene of Simian immunodeficiency virus
A gene of Ectromelia virus that has a protein-coding gene type
Bin Zhao, Oliver He
12643
protein-coding gene of Ectromelia virus
A gene of Rotavirus A that has a protein-coding gene type
Bin Zhao, Oliver He
28875
protein-coding gene of Rotavirus A
A gene of Bovine herpesvirus 5 that has a protein-coding gene type
Bin Zhao, Oliver He
35244
protein-coding gene of Bovine herpesvirus 5
A gene of Plasmodium falciparum 3D7 that has a protein-coding gene type
Bin Zhao, Oliver He
36329
protein-coding gene of Plasmodium falciparum 3D7
A gene of Rotavirus C that has a protein-coding gene type
Bin Zhao, Oliver He
36427
protein-coding gene of Rotavirus C
A gene of Autographa californica nucleopolyhedrovirus that has a protein-coding gene type
Bin Zhao, Oliver He
46015
protein-coding gene of Autographa californica nucleopolyhedrovirus
A gene of Haemophilus influenzae Rd KW20 that has a protein-coding gene type
Bin Zhao, Oliver He
71421
protein-coding gene of Haemophilus influenzae Rd KW20
A gene of Mycobacterium tuberculosis CDC1551 that has a protein-coding gene type
Bin Zhao, Oliver He
83331
protein-coding gene of Mycobacterium tuberculosis CDC1551
A gene of Mycobacterium tuberculosis H37Rv that has a protein-coding gene type
Bin Zhao, Oliver He
83332
protein-coding gene of Mycobacterium tuberculosis H37Rv
A gene of Porcine circovirus 2 that has a protein-coding gene type
Bin Zhao, Oliver He
85708
protein-coding gene of Porcine circovirus 2
A gene of Helicobacter pylori 26695 that has a protein-coding gene type
Bin Zhao, Oliver He
85962
protein-coding gene of Helicobacter pylori 26695
A gene of Helicobacter pylori J99 that has a protein-coding gene type
Bin Zhao, Oliver He
85963
protein-coding gene of Helicobacter pylori J99
A gene of Staphylococcus aureus subsp. aureus NCTC 8325 that has a protein-coding gene type
Bin Zhao, Oliver He
93061
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
Bin Zhao, Oliver He
93838
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
Bin Zhao, Oliver He
99287
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
Bin Zhao, Oliver He
115713
protein-coding gene of Chlamydophila pneumoniae CWL029
A gene of Neisseria meningitidis MC58 that has a protein-coding gene type
Bin Zhao, Oliver He
122586
protein-coding gene of Neisseria meningitidis MC58
A gene of Neisseria meningitidis Z2491 that has a protein-coding gene type
Bin Zhao, Oliver He
122587
protein-coding gene of Neisseria meningitidis Z2491
A gene of Chlamydophila pneumoniae J138 that has a protein-coding gene type
Bin Zhao, Oliver He
138677
protein-coding gene of Chlamydophila pneumoniae J138
A gene of Escherichia coli O157:H7 str. EDL933 that has a protein-coding gene type
Bin Zhao, Oliver He
155864
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
Bin Zhao, Oliver He
158878
protein-coding gene of Staphylococcus aureus subsp. aureus Mu50
A gene of Staphylococcus aureus subsp. aureus N315 that has a protein-coding gene type
Bin Zhao, Oliver He
158879
protein-coding gene of Staphylococcus aureus subsp. aureus N315
A gene of Streptococcus pyogenes M1 GAS that has a protein-coding gene type
Bin Zhao, Oliver He
160490
protein-coding gene of Streptococcus pyogenes M1 GAS
A gene of Streptococcus pyogenes str. Manfredo that has a protein-coding gene type
Bin Zhao, Oliver He
160491
protein-coding gene of Streptococcus pyogenes str. Manfredo
A gene of Listeria monocytogenes EGD-e that has a protein-coding gene type
Bin Zhao, Oliver He
169963
protein-coding gene of Listeria monocytogenes EGD-e
A gene of Streptococcus pneumoniae TIGR4 that has a protein-coding gene type
Bin Zhao, Oliver He
170187
protein-coding gene of Streptococcus pneumoniae TIGR4
A gene of Streptococcus pneumoniae R6 that has a protein-coding gene type
Bin Zhao, Oliver He
171101
protein-coding gene of Streptococcus pneumoniae R6
A gene of Francisella tularensis subsp. tularensis SCHU S4 that has a protein-coding gene type
Bin Zhao, Oliver He
177416
protein-coding gene of Francisella tularensis subsp. tularensis SCHU S4
A gene of Chlamydophila pneumoniae TW-183 that has a protein-coding gene type
Bin Zhao, Oliver He
182082
protein-coding gene of Chlamydophila pneumoniae TW-183
A gene of Streptococcus pyogenes MGAS8232 that has a protein-coding gene type
Bin Zhao, Oliver He
186103
protein-coding gene of Streptococcus pyogenes MGAS8232
A gene of Yersinia pestis KIM10+ that has a protein-coding gene type
Bin Zhao, Oliver He
187410
protein-coding gene of Yersinia pestis KIM10+
A gene of Leptospira interrogans serovar Lai str. 56601 that has a protein-coding gene type
Bin Zhao, Oliver He
189518
protein-coding gene of Leptospira interrogans serovar Lai str. 56601
A gene of Bacillus anthracis str. A2012 that has a protein-coding gene type
Bin Zhao, Oliver He
191218
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
Bin Zhao, Oliver He
192222
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
Bin Zhao, Oliver He
193567
protein-coding gene of Streptococcus pyogenes SSI-1
A gene of Campylobacter jejuni RM1221 that has a protein-coding gene type
Bin Zhao, Oliver He
195099
protein-coding gene of Campylobacter jejuni RM1221
A gene of Clostridium perfringens str. 13 that has a protein-coding gene type
Bin Zhao, Oliver He
195102
protein-coding gene of Clostridium perfringens str. 13
A gene of Clostridium perfringens ATCC 13124 that has a protein-coding gene type
Bin Zhao, Oliver He
195103
protein-coding gene of Clostridium perfringens ATCC 13124
A gene of Staphylococcus aureus subsp. aureus MW2 that has a protein-coding gene type
Bin Zhao, Oliver He
196620
protein-coding gene of Staphylococcus aureus subsp. aureus MW2
A gene of Bacillus anthracis str. Ames that has a protein-coding gene type
Bin Zhao, Oliver He
198094
protein-coding gene of Bacillus anthracis str. Ames
A gene of Shigella flexneri 2a str. 301 that has a protein-coding gene type
Bin Zhao, Oliver He
198214
protein-coding gene of Shigella flexneri 2a str. 301
A gene of Shigella flexneri 2a str. 2457T that has a protein-coding gene type
Bin Zhao, Oliver He
198215
protein-coding gene of Shigella flexneri 2a str. 2457T
A gene of Streptococcus pyogenes MGAS315 that has a protein-coding gene type
Bin Zhao, Oliver He
198466
protein-coding gene of Streptococcus pyogenes MGAS315
A gene of Escherichia coli CFT073 that has a protein-coding gene type
Bin Zhao, Oliver He
199310
protein-coding gene of Escherichia coli CFT073
A gene of Brucella suis 1330 that has a protein-coding gene type
Bin Zhao, Oliver He
204722
protein-coding gene of Brucella suis 1330
A gene of Streptococcus agalactiae A909 that has a protein-coding gene type
Bin Zhao, Oliver He
205921
protein-coding gene of Streptococcus agalactiae A909
A gene of Streptococcus agalactiae 2603V/R that has a protein-coding gene type
Bin Zhao, Oliver He
208435
protein-coding gene of Streptococcus agalactiae 2603V/R
A gene of Pseudomonas aeruginosa UCBPP-PA14 that has a protein-coding gene type
Bin Zhao, Oliver He
208963
protein-coding gene of Pseudomonas aeruginosa UCBPP-PA14
A gene of Pseudomonas aeruginosa PAO1 that has a protein-coding gene type
Bin Zhao, Oliver He
208964
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
Bin Zhao, Oliver He
211044
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
Bin Zhao, Oliver He
211110
protein-coding gene of Streptococcus agalactiae NEM316
A gene of Clostridium tetani E88 that has a protein-coding gene type
Bin Zhao, Oliver He
212717
protein-coding gene of Clostridium tetani E88
A gene of Yersinia pestis CO92 that has a protein-coding gene type
Bin Zhao, Oliver He
214092
protein-coding gene of Yersinia pestis CO92
A gene of Cryptococcus neoformans var. neoformans JEC21 that has a protein-coding gene type
Bin Zhao, Oliver He
214684
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
Bin Zhao, Oliver He
220341
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
Bin Zhao, Oliver He
224326
protein-coding gene of Borrelia burgdorferi B31
A gene of Brucella melitensis bv. 1 str. 16M that has a protein-coding gene type
Bin Zhao, Oliver He
224914
protein-coding gene of Brucella melitensis bv. 1 str. 16M
A gene of Enterococcus faecalis V583 that has a protein-coding gene type
Bin Zhao, Oliver He
226185
protein-coding gene of Enterococcus faecalis V583
A gene of Aspergillus nidulans FGSC A4 that has a protein-coding gene type
Bin Zhao, Oliver He
227321
protein-coding gene of Aspergillus nidulans FGSC A4
A gene of Coxiella burnetii RSA 493 that has a protein-coding gene type
Bin Zhao, Oliver He
227377
protein-coding gene of Coxiella burnetii RSA 493
A gene of Yersinia pestis biovar Microtus str. 91001 that has a protein-coding gene type
Bin Zhao, Oliver He
229193
protein-coding gene of Yersinia pestis biovar Microtus str. 91001
A gene of Candida albicans SC5314 that has a protein-coding gene type
Bin Zhao, Oliver He
237561
protein-coding gene of Candida albicans SC5314
A gene of Burkholderia mallei ATCC 23344 that has a protein-coding gene type
Bin Zhao, Oliver He
243160
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
Bin Zhao, Oliver He
243277
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
Bin Zhao, Oliver He
257309
protein-coding gene of Corynebacterium diphtheriae NCTC 13129
A gene of Bordetella bronchiseptica RB50 that has a protein-coding gene type
Bin Zhao, Oliver He
257310
protein-coding gene of Bordetella bronchiseptica RB50
A gene of Bordetella pertussis Tohama I that has a protein-coding gene type
Bin Zhao, Oliver He
257313
protein-coding gene of Bordetella pertussis Tohama I
A gene of Bacillus anthracis str. Sterne that has a protein-coding gene type
Bin Zhao, Oliver He
260799
protein-coding gene of Bacillus anthracis str. Sterne
A gene of Bacillus anthracis str. 'Ames Ancestor' that has a protein-coding gene type
Bin Zhao, Oliver He
261594
protein-coding gene of Bacillus anthracis str. 'Ames Ancestor'
A gene of Orgyia pseudotsugata MNPV that has a protein-coding gene type
Bin Zhao, Oliver He
262177
protein-coding gene of Orgyia pseudotsugata MNPV
A gene of Mycobacterium avium subsp. paratuberculosis K-10 that has a protein-coding gene type
Bin Zhao, Oliver He
262316
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
Bin Zhao, Oliver He
265669
protein-coding gene of Listeria monocytogenes serotype 4b str. F2365
A gene of Bombyx mori NPV that has a protein-coding gene type
Bin Zhao, Oliver He
271108
protein-coding gene of Bombyx mori NPV
A gene of Burkholderia pseudomallei K96243 that has a protein-coding gene type
Bin Zhao, Oliver He
272560
protein-coding gene of Burkholderia pseudomallei K96243
A gene of Chlamydia trachomatis D/UW-3/CX that has a protein-coding gene type
Bin Zhao, Oliver He
272561
protein-coding gene of Chlamydia trachomatis D/UW-3/CX
A gene of Clostridium difficile 630 that has a protein-coding gene type
Bin Zhao, Oliver He
272563
protein-coding gene of Clostridium difficile 630
A gene of Legionella pneumophila subsp. pneumophila str. Philadelphia 1 that has a protein-coding gene type
Bin Zhao, Oliver He
272624
protein-coding gene of Legionella pneumophila subsp. pneumophila str. Philadelphia 1
A gene of Neisseria meningitidis FAM18 that has a protein-coding gene type
Bin Zhao, Oliver He
272831
protein-coding gene of Neisseria meningitidis FAM18
A gene of Pasteurella multocida subsp. multocida str. Pm70 that has a protein-coding gene type
Bin Zhao, Oliver He
272843
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
Bin Zhao, Oliver He
272947
protein-coding gene of Rickettsia prowazekii str. Madrid E
A gene of Staphylococcus aureus RF122 that has a protein-coding gene type
Bin Zhao, Oliver He
273036
protein-coding gene of Staphylococcus aureus RF122
A gene of Yersinia pseudotuberculosis IP 32953 that has a protein-coding gene type
Bin Zhao, Oliver He
273123
protein-coding gene of Yersinia pseudotuberculosis IP 32953
A gene of Haemophilus influenzae 86-028NP that has a protein-coding gene type
Bin Zhao, Oliver He
281310
protein-coding gene of Haemophilus influenzae 86-028NP
A gene of Staphylococcus aureus subsp. aureus MRSA252 that has a protein-coding gene type
Bin Zhao, Oliver He
282458
protein-coding gene of Staphylococcus aureus subsp. aureus MRSA252
A gene of Bartonella henselae str. Houston-1 that has a protein-coding gene type
Bin Zhao, Oliver He
283166
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
Bin Zhao, Oliver He
283643
protein-coding gene of Cryptococcus neoformans var. neoformans B-3501A
A gene of Candida glabrata CBS 138 that has a protein-coding gene type
Bin Zhao, Oliver He
284593
protein-coding gene of Candida glabrata CBS 138
A gene of Streptococcus pyogenes MGAS10394 that has a protein-coding gene type
Bin Zhao, Oliver He
286636
protein-coding gene of Streptococcus pyogenes MGAS10394
A gene of Clostridium perfringens SM101 that has a protein-coding gene type
Bin Zhao, Oliver He
289380
protein-coding gene of Clostridium perfringens SM101
A gene of Streptococcus pyogenes MGAS5005 that has a protein-coding gene type
Bin Zhao, Oliver He
293653
protein-coding gene of Streptococcus pyogenes MGAS5005
A gene of Entamoeba histolytica HM-1:IMSS that has a protein-coding gene type
Bin Zhao, Oliver He
294381
protein-coding gene of Entamoeba histolytica HM-1:IMSS
A gene of Legionella pneumophila str. Lens that has a protein-coding gene type
Bin Zhao, Oliver He
297245
protein-coding gene of Legionella pneumophila str. Lens
A gene of Legionella pneumophila str. Paris that has a protein-coding gene type
Bin Zhao, Oliver He
297246
protein-coding gene of Legionella pneumophila str. Paris
A gene of Shigella dysenteriae Sd197 that has a protein-coding gene type
Bin Zhao, Oliver He
300267
protein-coding gene of Shigella dysenteriae Sd197
A gene of Shigella boydii Sb227 that has a protein-coding gene type
Bin Zhao, Oliver He
300268
protein-coding gene of Shigella boydii Sb227
A gene of Shigella sonnei Ss046 that has a protein-coding gene type
Bin Zhao, Oliver He
300269
protein-coding gene of Shigella sonnei Ss046
A gene of Escherichia coli str. K-12 substr. DH10B that has a protein-coding gene type
Bin Zhao, Oliver He
316385
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
Bin Zhao, Oliver He
316401
protein-coding gene of Escherichia coli ETEC H10407
A gene of Streptococcus pyogenes MGAS6180 that has a protein-coding gene type
Bin Zhao, Oliver He
319701
protein-coding gene of Streptococcus pyogenes MGAS6180
A gene of Burkholderia pseudomallei 1710b that has a protein-coding gene type
Bin Zhao, Oliver He
320372
protein-coding gene of Burkholderia pseudomallei 1710b
A gene of Burkholderia pseudomallei 668 that has a protein-coding gene type
Bin Zhao, Oliver He
320373
protein-coding gene of Burkholderia pseudomallei 668
A gene of Burkholderia mallei SAVP1 that has a protein-coding gene type
Bin Zhao, Oliver He
320388
protein-coding gene of Burkholderia mallei SAVP1
A gene of Burkholderia mallei NCTC 10247 that has a protein-coding gene type
Bin Zhao, Oliver He
320389
protein-coding gene of Burkholderia mallei NCTC 10247
A gene of Aspergillus fumigatus Af293 that has a protein-coding gene type
Bin Zhao, Oliver He
330879
protein-coding gene of Aspergillus fumigatus Af293
A gene of Escherichia coli E24377A that has a protein-coding gene type
Bin Zhao, Oliver He
331111
protein-coding gene of Escherichia coli E24377A
A gene of Escherichia coli HS that has a protein-coding gene type
Bin Zhao, Oliver He
331112
protein-coding gene of Escherichia coli HS
A gene of Mycobacterium tuberculosis F11 that has a protein-coding gene type
Bin Zhao, Oliver He
336982
protein-coding gene of Mycobacterium tuberculosis F11
A gene of Shigella boydii CDC 3083-94 that has a protein-coding gene type
Bin Zhao, Oliver He
344609
protein-coding gene of Shigella boydii CDC 3083-94
A gene of Vibrio cholerae O395 that has a protein-coding gene type
Bin Zhao, Oliver He
345073
protein-coding gene of Vibrio cholerae O395
A gene of Leishmania major strain Friedlin that has a protein-coding gene type
Bin Zhao, Oliver He
347515
protein-coding gene of Leishmania major strain Friedlin
A gene of Yersinia pestis Angola that has a protein-coding gene type
Bin Zhao, Oliver He
349746
protein-coding gene of Yersinia pestis Angola
A gene of Yersinia pseudotuberculosis IP 31758 that has a protein-coding gene type
Bin Zhao, Oliver He
349747
protein-coding gene of Yersinia pseudotuberculosis IP 31758
A gene of Plasmodium yoelii yoelii 17XNL that has a protein-coding gene type
Bin Zhao, Oliver He
352914
protein-coding gene of Plasmodium yoelii yoelii 17XNL
A gene of Cryptosporidium parvum Iowa II that has a protein-coding gene type
Bin Zhao, Oliver He
353152
protein-coding gene of Cryptosporidium parvum Iowa II
A gene of Trypanosoma cruzi strain CL Brener that has a protein-coding gene type
Bin Zhao, Oliver He
353153
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
Bin Zhao, Oliver He
354242
protein-coding gene of Campylobacter jejuni subsp. jejuni 81-176
A gene of Burkholderia pseudomallei 1106a that has a protein-coding gene type
Bin Zhao, Oliver He
357348
protein-coding gene of Burkholderia pseudomallei 1106a
A gene of Brucella melitensis biovar Abortus 2308 that has a protein-coding gene type
Bin Zhao, Oliver He
359391
protein-coding gene of Brucella melitensis biovar Abortus 2308
A gene of Bartonella bacilliformis KC583 that has a protein-coding gene type
Bin Zhao, Oliver He
360095
protein-coding gene of Bartonella bacilliformis KC583
A gene of Yersinia pestis Antiqua that has a protein-coding gene type
Bin Zhao, Oliver He
360102
protein-coding gene of Yersinia pestis Antiqua
A gene of Campylobacter jejuni subsp. doylei 269.97 that has a protein-coding gene type
Bin Zhao, Oliver He
360109
protein-coding gene of Campylobacter jejuni subsp. doylei 269.97
A gene of Bordetella avium 197N that has a protein-coding gene type
Bin Zhao, Oliver He
360910
protein-coding gene of Bordetella avium 197N
A gene of Escherichia coli 536 that has a protein-coding gene type
Bin Zhao, Oliver He
362663
protein-coding gene of Escherichia coli 536
A gene of Escherichia coli UTI89 that has a protein-coding gene type
Bin Zhao, Oliver He
364106
protein-coding gene of Escherichia coli UTI89
A gene of Streptococcus pyogenes MGAS9429 that has a protein-coding gene type
Bin Zhao, Oliver He
370551
protein-coding gene of Streptococcus pyogenes MGAS9429
A gene of Streptococcus pyogenes MGAS10270 that has a protein-coding gene type
Bin Zhao, Oliver He
370552
protein-coding gene of Streptococcus pyogenes MGAS10270
A gene of Streptococcus pyogenes MGAS2096 that has a protein-coding gene type
Bin Zhao, Oliver He
370553
protein-coding gene of Streptococcus pyogenes MGAS2096
A gene of Streptococcus pyogenes MGAS10750 that has a protein-coding gene type
Bin Zhao, Oliver He
370554
protein-coding gene of Streptococcus pyogenes MGAS10750
A gene of Streptococcus pneumoniae D39 that has a protein-coding gene type
Bin Zhao, Oliver He
373153
protein-coding gene of Streptococcus pneumoniae D39
A gene of Shigella flexneri 5 str. 8401 that has a protein-coding gene type
Bin Zhao, Oliver He
373384
protein-coding gene of Shigella flexneri 5 str. 8401
A gene of Neisseria meningitidis 053442 that has a protein-coding gene type
Bin Zhao, Oliver He
374833
protein-coding gene of Neisseria meningitidis 053442
A gene of Francisella tularensis subsp. holarctica LVS that has a protein-coding gene type
Bin Zhao, Oliver He
376619
protein-coding gene of Francisella tularensis subsp. holarctica LVS
A gene of Escherichia coli O26:H- that has a protein-coding gene type
Bin Zhao, Oliver He
376724
protein-coding gene of Escherichia coli O26:H-
A gene of Yersinia pestis Nepal516 that has a protein-coding gene type
Bin Zhao, Oliver He
377628
protein-coding gene of Yersinia pestis Nepal516
A gene of Aeromonas salmonicida subsp. salmonicida A449 that has a protein-coding gene type
Bin Zhao, Oliver He
382245
protein-coding gene of Aeromonas salmonicida subsp. salmonicida A449
A gene of Bartonella tribocorum CIP 105476 that has a protein-coding gene type
Bin Zhao, Oliver He
382640
protein-coding gene of Bartonella tribocorum CIP 105476
A gene of Escherichia coli O157:H7 str. Sakai that has a protein-coding gene type
Bin Zhao, Oliver He
386585
protein-coding gene of Escherichia coli O157:H7 str. Sakai
A gene of Yersinia pestis Pestoides F that has a protein-coding gene type
Bin Zhao, Oliver He
386656
protein-coding gene of Yersinia pestis Pestoides F
A gene of Yersinia enterocolitica subsp. enterocolitica 8081 that has a protein-coding gene type
Bin Zhao, Oliver He
393305
protein-coding gene of Yersinia enterocolitica subsp. enterocolitica 8081
A gene of Legionella pneumophila str. Corby that has a protein-coding gene type
Bin Zhao, Oliver He
400673
protein-coding gene of Legionella pneumophila str. Corby
A gene of Escherichia coli APEC O1 that has a protein-coding gene type
Bin Zhao, Oliver He
405955
protein-coding gene of Escherichia coli APEC O1
A gene of Campylobacter jejuni subsp. jejuni 81116 that has a protein-coding gene type
Bin Zhao, Oliver He
407148
protein-coding gene of Campylobacter jejuni subsp. jejuni 81116
A gene of Escherichia coli SE11 that has a protein-coding gene type
Bin Zhao, Oliver He
409438
protein-coding gene of Escherichia coli SE11
A gene of Burkholderia mallei NCTC 10229 that has a protein-coding gene type
Bin Zhao, Oliver He
412022
protein-coding gene of Burkholderia mallei NCTC 10229
A gene of Yersinia pestis CA88-4125 that has a protein-coding gene type
Bin Zhao, Oliver He
412420
protein-coding gene of Yersinia pestis CA88-4125
A gene of Escherichia coli B str. REL606 that has a protein-coding gene type
Bin Zhao, Oliver He
413997
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
Bin Zhao, Oliver He
416269
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
Bin Zhao, Oliver He
418127
protein-coding gene of Staphylococcus aureus subsp. aureus Mu3
A gene of Mycobacterium tuberculosis H37Ra that has a protein-coding gene type
Bin Zhao, Oliver He
419947
protein-coding gene of Mycobacterium tuberculosis H37Ra
A gene of Legionella pneumophila 2300/99 Alcoy that has a protein-coding gene type
Bin Zhao, Oliver He
423212
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
Bin Zhao, Oliver He
426430
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
Bin Zhao, Oliver He
434271
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
Bin Zhao, Oliver He
439855
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
Bin Zhao, Oliver He
441770
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
Bin Zhao, Oliver He
441771
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
Bin Zhao, Oliver He
444450
protein-coding gene of Escherichia coli O157:H7 str. EC4115
A gene of Borrelia burgdorferi 156a that has a protein-coding gene type
Bin Zhao, Oliver He
445983
protein-coding gene of Borrelia burgdorferi 156a
A gene of Borrelia burgdorferi ZS7 that has a protein-coding gene type
Bin Zhao, Oliver He
445985
protein-coding gene of Borrelia burgdorferi ZS7
A gene of Francisella tularensis subsp. holarctica FTNF002-00 that has a protein-coding gene type
Bin Zhao, Oliver He
458234
protein-coding gene of Francisella tularensis subsp. holarctica FTNF002-00
A gene of Streptococcus pyogenes NZ131 that has a protein-coding gene type
Bin Zhao, Oliver He
471876
protein-coding gene of Streptococcus pyogenes NZ131
A gene of Paenibacillus sp. Y412MC10 that has a protein-coding gene type
Bin Zhao, Oliver He
481743
protein-coding gene of Paenibacillus sp. Y412MC10
A gene of Streptococcus pneumoniae Taiwan19F-14 that has a protein-coding gene type
Bin Zhao, Oliver He
487213
protein-coding gene of Streptococcus pneumoniae Taiwan19F-14
A gene of Streptococcus pneumoniae Hungary19A-6 that has a protein-coding gene type
Bin Zhao, Oliver He
487214
protein-coding gene of Streptococcus pneumoniae Hungary19A-6
A gene of Streptococcus pneumoniae 70585 that has a protein-coding gene type
Bin Zhao, Oliver He
488221
protein-coding gene of Streptococcus pneumoniae 70585
A gene of Streptococcus pneumoniae JJA that has a protein-coding gene type
Bin Zhao, Oliver He
488222
protein-coding gene of Streptococcus pneumoniae JJA
A gene of Streptococcus pneumoniae P1031 that has a protein-coding gene type
Bin Zhao, Oliver He
488223
protein-coding gene of Streptococcus pneumoniae P1031
A gene of Clostridium botulinum B1 str. Okra that has a protein-coding gene type
Bin Zhao, Oliver He
498213
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
Bin Zhao, Oliver He
498214
protein-coding gene of Clostridium botulinum A3 str. Loch Maree
A gene of Edwardsiella tarda EIB202 that has a protein-coding gene type
Bin Zhao, Oliver He
498217
protein-coding gene of Edwardsiella tarda EIB202
A gene of Yersinia pseudotuberculosis YPIII that has a protein-coding gene type
Bin Zhao, Oliver He
502800
protein-coding gene of Yersinia pseudotuberculosis YPIII
A gene of Yersinia pseudotuberculosis PB1/+ that has a protein-coding gene type
Bin Zhao, Oliver He
502801
protein-coding gene of Yersinia pseudotuberculosis PB1/+
A gene of Clostridium botulinum E3 str. Alaska E43 that has a protein-coding gene type
Bin Zhao, Oliver He
508767
protein-coding gene of Clostridium botulinum E3 str. Alaska E43
A gene of Toxoplasma gondii ME49 that has a protein-coding gene type
Bin Zhao, Oliver He
508771
protein-coding gene of Toxoplasma gondii ME49
A gene of Escherichia coli str. K-12 substr. MG1655 that has a protein-coding gene type
Bin Zhao, Oliver He
511145
protein-coding gene of Escherichia coli str. K-12 substr. MG1655
A gene of Streptococcus pneumoniae G54 that has a protein-coding gene type
Bin Zhao, Oliver He
512566
protein-coding gene of Streptococcus pneumoniae G54
A gene of Streptococcus pneumoniae CGSP14 that has a protein-coding gene type
Bin Zhao, Oliver He
516950
protein-coding gene of Streptococcus pneumoniae CGSP14
A gene of Borrelia burgdorferi N40 that has a protein-coding gene type
Bin Zhao, Oliver He
521007
protein-coding gene of Borrelia burgdorferi N40
A gene of Borrelia burgdorferi 297 that has a protein-coding gene type
Bin Zhao, Oliver He
521009
protein-coding gene of Borrelia burgdorferi 297
A gene of Burkholderia pseudomallei MSHR346 that has a protein-coding gene type
Bin Zhao, Oliver He
536230
protein-coding gene of Burkholderia pseudomallei MSHR346
A gene of Actinobacillus pleuropneumoniae serovar 7 str. AP76 that has a protein-coding gene type
Bin Zhao, Oliver He
537457
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
Bin Zhao, Oliver He
544404
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
Bin Zhao, Oliver He
552526
protein-coding gene of Streptococcus equi subsp. zooepidemicus MGCS10565
A gene of Listeria monocytogenes HCC23 that has a protein-coding gene type
Bin Zhao, Oliver He
552536
protein-coding gene of Listeria monocytogenes HCC23
A gene of Pseudomonas aeruginosa LESB58 that has a protein-coding gene type
Bin Zhao, Oliver He
557722
protein-coding gene of Pseudomonas aeruginosa LESB58
A gene of Saccharomyces cerevisiae S288c that has a protein-coding gene type
Bin Zhao, Oliver He
559292
protein-coding gene of Saccharomyces cerevisiae S288c
A gene of Streptococcus pneumoniae ATCC 700669 that has a protein-coding gene type
Bin Zhao, Oliver He
561276
protein-coding gene of Streptococcus pneumoniae ATCC 700669
A gene of Helicobacter pylori G27 that has a protein-coding gene type
Bin Zhao, Oliver He
563041
protein-coding gene of Helicobacter pylori G27
A gene of Escherichia coli Vir68 that has a protein-coding gene type
Bin Zhao, Oliver He
563770
protein-coding gene of Escherichia coli Vir68
A gene of Bacillus anthracis str. CDC 684 that has a protein-coding gene type
Bin Zhao, Oliver He
568206
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
Bin Zhao, Oliver He
568819
protein-coding gene of Listeria monocytogenes serotype 4b str. CLIP 80459
A gene of Helicobacter pylori P12 that has a protein-coding gene type
Bin Zhao, Oliver He
570508
protein-coding gene of Helicobacter pylori P12
A gene of Escherichia coli O26:H11 str. 11368 that has a protein-coding gene type
Bin Zhao, Oliver He
573235
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
Bin Zhao, Oliver He
574521
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
Bin Zhao, Oliver He
579112
protein-coding gene of Vibrio cholerae M66-2
A gene of Escherichia coli IAI1 that has a protein-coding gene type
Bin Zhao, Oliver He
585034
protein-coding gene of Escherichia coli IAI1
A gene of Escherichia coli S88 that has a protein-coding gene type
Bin Zhao, Oliver He
585035
protein-coding gene of Escherichia coli S88
A gene of Escherichia coli 55989 that has a protein-coding gene type
Bin Zhao, Oliver He
585055
protein-coding gene of Escherichia coli 55989
A gene of Escherichia coli UMN026 that has a protein-coding gene type
Bin Zhao, Oliver He
585056
protein-coding gene of Escherichia coli UMN026
A gene of Escherichia coli IAI39 that has a protein-coding gene type
Bin Zhao, Oliver He
585057
protein-coding gene of Escherichia coli IAI39
A gene of Escherichia coli O103:H2 str. 12009 that has a protein-coding gene type
Bin Zhao, Oliver He
585395
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
Bin Zhao, Oliver He
585396
protein-coding gene of Escherichia coli O111:H- str. 11128
A gene of Escherichia coli ED1a that has a protein-coding gene type
Bin Zhao, Oliver He
585397
protein-coding gene of Escherichia coli ED1a
A gene of Bacillus anthracis str. A0248 that has a protein-coding gene type
Bin Zhao, Oliver He
592021
protein-coding gene of Bacillus anthracis str. A0248
A gene of Helicobacter pylori B38 that has a protein-coding gene type
Bin Zhao, Oliver He
592205
protein-coding gene of Helicobacter pylori B38
A gene of Escherichia coli BW2952 that has a protein-coding gene type
Bin Zhao, Oliver He
595496
protein-coding gene of Escherichia coli BW2952
A gene of Listeria monocytogenes 08-5923 that has a protein-coding gene type
Bin Zhao, Oliver He
637381
protein-coding gene of Listeria monocytogenes 08-5923
A gene of Listeria monocytogenes 08-5578 that has a protein-coding gene type
Bin Zhao, Oliver He
653938
protein-coding gene of Listeria monocytogenes 08-5578
A gene of Neisseria meningitidis alpha14 that has a protein-coding gene type
Bin Zhao, Oliver He
662598
protein-coding gene of Neisseria meningitidis alpha14
A gene of Staphylococcus aureus subsp. aureus ED98 that has a protein-coding gene type
Bin Zhao, Oliver He
681288
protein-coding gene of Staphylococcus aureus subsp. aureus ED98
A gene of Mycoplasma gallisepticum str. R(low) that has a protein-coding gene type
Bin Zhao, Oliver He
710127
protein-coding gene of Mycoplasma gallisepticum str. R(low)
A gene of Feline infectious peritonitis virus that has a pseudo gene type
Bin Zhao, Oliver He
11135
pseudo gene of Feline infectious peritonitis virus
A gene of Haemophilus influenzae Rd KW20 that has a pseudo gene type
Bin Zhao, Oliver He
71421
pseudo gene of Haemophilus influenzae Rd KW20
A gene of Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 that has a pseudo gene type
Bin Zhao, Oliver He
99287
pseudo gene of Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
A gene of Streptococcus pneumoniae TIGR4 that has a pseudo gene type
Bin Zhao, Oliver He
170187
pseudo gene of Streptococcus pneumoniae TIGR4
A gene of Francisella tularensis subsp. tularensis SCHU S4 that has a pseudo gene type
Bin Zhao, Oliver He
177416
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
Bin Zhao, Oliver He
192222
pseudo gene of Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
A gene of Brucella suis 1330 that has a pseudo gene type
Bin Zhao, Oliver He
204722
pseudo gene of Brucella suis 1330
A gene of Vibrio cholerae O1 biovar El Tor str. N16961 that has a pseudo gene type
Bin Zhao, Oliver He
243277
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
Bin Zhao, Oliver He
265669
pseudo gene of Listeria monocytogenes serotype 4b str. F2365
A gene of Clostridium difficile 630 that has a pseudo gene type
Bin Zhao, Oliver He
272563
pseudo gene of Clostridium difficile 630
A gene of Brucella melitensis biovar Abortus 2308 that has a pseudo gene type
Bin Zhao, Oliver He
359391
pseudo gene of Brucella melitensis biovar Abortus 2308
A gene of Neisseria meningitidis 053442 that has a pseudo gene type
Bin Zhao, Oliver He
374833
pseudo gene of Neisseria meningitidis 053442
A gene of Francisella tularensis subsp. holarctica LVS that has a pseudo gene type
Bin Zhao, Oliver He
376619
pseudo gene of Francisella tularensis subsp. holarctica LVS
A gene of Aeromonas salmonicida subsp. salmonicida A449 that has a pseudo gene type
Bin Zhao, Oliver He
382245
pseudo gene of Aeromonas salmonicida subsp. salmonicida A449
A gene of Escherichia coli IAI39 that has a pseudo gene type
Bin Zhao, Oliver He
585057
pseudo gene of Escherichia coli IAI39
A gene of Yersinia pestis CO92 that has a miscRNA gene type
Bin Zhao, Oliver He
214092
miscRNA gene of Yersinia pestis CO92
A gene of Yersinia pestis biovar Microtus str. 91001 that has a miscRNA gene type
Bin Zhao, Oliver He
229193
miscRNA gene of Yersinia pestis biovar Microtus str. 91001
A gene of Yersinia pestis Angola that has a miscRNA gene type
Bin Zhao, Oliver He
349746
miscRNA gene of Yersinia pestis Angola
A gene of Yersinia pestis Antiqua that has a miscRNA gene type
Bin Zhao, Oliver He
360102
miscRNA gene of Yersinia pestis Antiqua
A gene of Yersinia pestis Nepal516 that has a miscRNA gene type
Bin Zhao, Oliver He
377628
miscRNA gene of Yersinia pestis Nepal516
A gene of Yersinia pestis Pestoides F that has a miscRNA gene type
Bin Zhao, Oliver He
386656
miscRNA gene of Yersinia pestis Pestoides F
A gene of Francisella tularensis subsp. tularensis SCHU S4 that has a RNA gene type
Bin Zhao, Oliver He
177416
RNA gene of Francisella tularensis subsp. tularensis SCHU S4
A gene of Yersinia pestis CO92 that has a RNA gene type
Bin Zhao, Oliver He
214092
RNA gene of Yersinia pestis CO92
A gene of Yersinia pestis biovar Microtus str. 91001 that has a RNA gene type
Bin Zhao, Oliver He
229193
RNA gene of Yersinia pestis biovar Microtus str. 91001
A gene of Yersinia pestis Angola that has a RNA gene type
Bin Zhao, Oliver He
349746
RNA gene of Yersinia pestis Angola
A gene of Yersinia pestis Antiqua that has a RNA gene type
Bin Zhao, Oliver He
360102
RNA gene of Yersinia pestis Antiqua
A gene of Francisella tularensis subsp. holarctica LVS that has a RNA gene type
Bin Zhao, Oliver He
376619
RNA gene of Francisella tularensis subsp. holarctica LVS
A gene of Yersinia pestis Nepal516 that has a RNA gene type
Bin Zhao, Oliver He
377628
RNA gene of Yersinia pestis Nepal516
A gene of Yersinia pestis Pestoides F that has a RNA gene type
Bin Zhao, Oliver He
386656
RNA gene of Yersinia pestis Pestoides F
A gene of Haemophilus influenzae Rd KW20 that has a other gene type
Bin Zhao, Oliver He
71421
gene of Haemophilus influenzae Rd KW20 with other gene type
A gene of Brucella suis 1330 that has a other gene type
Bin Zhao, Oliver He
204722
gene of Brucella suis 1330 with other gene type
A gene of Plasmodium yoelii yoelii 17XNL that has a other gene type
Bin Zhao, Oliver He
352914
gene of Plasmodium yoelii yoelii 17XNL with other gene type
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
155459
HIV1gp3
20140406
11676
protein-coding
NCBI-supplied
PMID: 2059206; 7884893; 8523563; 8626571; 8924209; 9188594; 9362478; 9792705; 9811770; 9846577; 10074203; 10613270; 11158303; 11172097; 11278465; 11406603; 11780123; 12167863; 12368356; 12600646; 12719574; 12750511; 12808465; 12808466; 12809610; 12830140; 12840737; 12859895; 12914693; 12920286; 12970355; 14527406; 14528300; 14528301; 14557625; 14564014; 14614829; 14672928; 14722068; 14747572; 14966139; 14978281; 14999100; 15013426; 15054139; 15080177; 15116720; 15139295; 15141007; 15152192; 15156567; 15168739; 15177194; 15183343; 15245742; 15296757; 15296758; 15353294; 15367624; 15373943; 15383144; 15537645; 15574592; 15574593; 15578976; 15602725; 15611076; 15638724; 15781449; 15809227; 15989462; 16014920; 16035254; 16046164; 16146763; 16250885; 16303161; 16354571; 16414984; 16418394; 16460778; 16492778; 16501124; 16530799; 16580072; 16631224; 16636053; 16641889; 16678488; 16699599; 16731937; 16822376; 16920826; 16940537; 17020885; 17023652; 17038330; 17049578; 17067930; 17083721; 17121840; 17126871; 17135358; 17267497; 17272283; 17285170; 17303427; 17331040; 17338854; 17522211; 17522216; 17586316; 17598142; 17609216; 17660191; 17727729; 17824250; 17825339; 17869271; 17898068; 17916373; 17928335; 17967058; 17977970; 18023836; 18036235; 18082865; 18184715; 18187620; 18262674; 18272582; 18272764; 18299330; 18304004; 18326044; 18338854; 18366335; 18391217; 18414671; 18414697; 18419775; 18448538; 18495196; 18499212; 18501607; 18541215; 18562529; 18577210; 18596088; 18603011; 18604271; 18619467; 18639915; 18675436; 18680593; 18789977; 18806783; 18809921; 18819469; 18827027; 18836454; 18842592; 18846074; 18945781; 18971252; 18976462; 18976920; 18987139; 19004939; 19004943; 19008196; 19020832; 19036809; 19038776; 19050398; 19056509; 19057663; 19088851; 19105849; 19109396; 19128510; 19149577; 19149995; 19211937; 19216784; 19218568; 19297501; 19304304; 19324886; 19344514; 19357165; 19401538; 19487726; 19535447; 19535450; 19581596; 19588889; 19649317; 19669862; 19694548; 19717177; 19776130; 19826902; 19828612; 19837465; 19841153; 19887642; 19910370; 19923175; 19939923; 19944180; 20012521; 20015971; 20018238; 20096141; 20126615; 20147392; 20174454; 20219919; 20220118; 20299747; 20335268; 20363737; 20450485; 20463065; 20463080; 20519393; 20519396; 20532212; 20538015; 20571604; 20592083; 20610708; 20624919; 20638642; 20642434; 20686027; 20728451; 20809132; 20833716; 20844042; 20926562; 20939174; 20943965; 20971849; 21071676; 21084468; 21147461; 21147467; 21149631; 21152581; 21167246; 21182427; 21228271; 21239176; 21270145; 21279453; 21345952; 21370050; 21393191; 21480314; 21489586; 21569376; 21571098; 21734563; 21741003; 21752914; 21763503; 21763507; 21835787; 21874023; 21934670; 21994560; 22013041; 22017399; 22023594; 22190034; 22190036; 22190037; 22203821; 22205746; 22218868; 22286874; 22346743; 22347227; 22369580; 22379088; 22451677; 22479405; 22509177; 22553496; 22555953; 22590503; 22720156; 22725134; 22728817; 22767258; 22787460; 22807680; 22855686; 22894923; 22970171; 23001005; 23080486; 23098073; 23175372; 23316055; 23417613; 23469063; 23576497; 23689841; 23707381; 23988114; 24225024; 24402281; 24422669
MUTATION: A mutation in the vif gene reduces viral replication and infectivity in nonpermissive cells [PMID:15989462].
1918
p23
Other designations: Vif
vif
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
155807
HIV1gp4
20140406
11676
protein-coding
NCBI-supplied
PMID: 7474080; 7474100; 7494303; 7592727; 7666531; 7724608; 8195203; 8551605; 8800208; 9013886; 9094673; 9151883; 9188632; 9199338; 9261351; 9334723; 9362478; 9371639; 9436978; 9449720; 9463369; 9520381; 9525626; 9525900; 9560267; 9582382; 9621063; 9636371; 9685344; 9817747; 9846873; 9874563; 9882380; 10359081; 10438581; 10561576; 10620603; 10708425; 10713718; 10772949; 10775602; 10888643; 10888660; 10931842; 10933727; 10958988; 10964507; 10985253; 11000244; 11024150; 11087358; 11152524; 11175251; 11181702; 11193032; 11196199; 11223251; 11259200; 11426943; 11437653; 11531413; 11689055; 11691994; 11878934; 11935461; 12079361; 12084067; 12095993; 12096338; 12208951; 12228227; 12237292; 12359436; 12379213; 12404120; 12444143; 12457980; 12504543; 12510154; 12525641; 12525642; 12573582; 12634356; 12639957; 12642036; 12738771; 12750393; 12750404; 12788643; 12805458; 12853482; 12881522; 12881523; 14506268; 14751250; 14767062; 14972559; 15063744; 15096517; 15142377; 15142379; 15142380; 15142381; 15142382; 15166037; 15254189; 15265780; 15294897; 15302882; 15331702; 15353294; 15380361; 15449141; 15485898; 15578586; 15578977; 15611322; 15616007; 15638722; 15650754; 15659641; 15708996; 15725353; 15731250; 15780175; 15817944; 15832179; 15956545; 16103149; 16103171; 16103188; 16120388; 16243842; 16305395; 16306615; 16337983; 16338743; 16354571; 16429131; 16480911; 16492162; 16492778; 16511342; 16520893; 16571786; 16877301; 16923959; 16950655; 16956949; 16968670; 16969134; 16983346; 17020411; 17023015; 17090531; 17140287; 17172832; 17176760; 17210576; 17254575; 17304248; 17314515; 17328670; 17331040; 17344301; 17347016; 17349711; 17360488; 17409234; 17433108; 17475642; 17553868; 17553871; 17559673; 17560997; 17586316; 17586317; 17609381; 17620334; 17622316; 17626091; 17630831; 17652391; 17824250; 17855541; 17932108; 17967742; 18039376; 18060429; 18061232; 18082865; 18094160; 18160429; 18187620; 18220834; 18275585; 18295813; 18385244; 18414671; 18414697; 18417583; 18434400; 18445273; 18514189; 18524771; 18541215; 18577246; 18606781; 18614999; 18638397; 18829761; 18987145; 19013323; 19020832; 19149577; 19160543; 19204000; 19254034; 19275579; 19275580; 19275582; 19275583; 19275584; 19275585; 19275586; 19275587; 19275588; 19328187; 19338763; 19344781; 19458171; 19516896; 19559726; 19581932; 19625402; 19629466; 19655254; 19657269; 19667756; 19674438; 19692467; 19696076; 19726511; 19798433; 19803398; 19838296; 19883084; 19895210; 19925402; 20008788; 20012529; 20015032; 20018238; 20069611; 20089662; 20097875; 20145198; 20347598; 20380698; 20380700; 20392842; 20404718; 20446002; 20529298; 20558198; 20609246; 20614012; 20628092; 20628645; 20685659; 20719241; 20801175; 20824083; 20870715; 20877724; 20920334; 21072166; 21084468; 21318276; 21411754; 21489275; 21519849; 21526938; 21566118; 21645334; 21651489; 21704113; 21763498; 21816823; 21827382; 21874023; 21875947; 21918813; 21934670; 21957298; 21994772; 22023789; 22077140; 22094081; 22110766; 22171270; 22185200; 22190034; 22190037; 22274659; 22292079; 22403404; 22422068; 22438978; 22457629; 22509482; 22552851; 22590503; 22720156; 22727020; 22776683; 22832123; 23001849; 23017337; 23255807; 23453579; 23467037; 23612978; 23726848; 23842279; 23849790; 23874603; 24045107; 24116224; 24178031
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].
1919
p15
Other designations: Vpr
vpr
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
156110
HIV1gp9
20140406
11676
protein-coding
NCBI-supplied
PMID: 1527859; 1565858; 2014052; 2052609; 3118220; 7540194; 7588629; 7769669; 7797518; 7831289; 7853525; 7859737; 7871751; 7884893; 7902127; 7903128; 7912927; 7975260; 7982906; 7983750; 8035515; 8057354; 8086129; 8102828; 8108442; 8124721; 8151774; 8151786; 8178481; 8262036; 8331733; 8437228; 8480425; 8516299; 8598486; 8599214; 8599229; 8599760; 8612235; 8626429; 8636073; 8663223; 8681387; 8709227; 8709241; 8709288; 8765022; 8769094; 8794306; 8862424; 8871625; 8939608; 8994833; 9017839; 9032396; 9049297; 9049329; 9052838; 9070423; 9075929; 9096366; 9108086; 9110068; 9123874; 9139671; 9153233; 9168885; 9218412; 9247029; 9288906; 9299485; 9314527; 9344905; 9351809; 9362478; 9371615; 9384576; 9453574; 9473011; 9490697; 9564030; 9582271; 9586638; 9617893; 9620685; 9624170; 9656992; 9705913; 9736718; 9778343; 9792838; 9811606; 9811611; 9920849; 9923610; 9971776; 10074203; 10196292; 10199403; 10208934; 10224289; 10339411; 10364375; 10366557; 10366564; 10375525; 10375528; 10388525; 10388555; 10393966; 10394361; 10403641; 10415019; 10417813; 10451539; 10470075; 10544125; 10547288; 10559302; 10574946; 10597774; 10607567; 10618429; 10636480; 10642173; 10684310; 10707087; 10713183; 10748182; 10753665; 10799608; 10807905; 10814565; 10906142; 10982373; 10985305; 11000208; 11006130; 11023665; 11070003; 11122241; 11123279; 11137132; 11153078; 11160719; 11177389; 11180285; 11208076; 11222731; 11251883; 11264384; 11264386; 11285224; 11289809; 11298321; 11298454; 11312657; 11323689; 11328823; 11331585; 11396948; 11420046; 11438519; 11448168; 11463741; 11500821; 11519482; 11525746; 11533201; 11578695; 11581379; 11593029; 11602047; 11602785; 11675348; 11689886; 11726657; 11810028; 11825573; 11847276; 11861836; 11884542; 11922627; 11932428; 11956293; 11958689; 11969293; 11976726; 12009866; 12032142; 12033791; 12058068; 12076760; 12097566; 12241561; 12270545; 12354773; 12359436; 12370346; 12396456; 12414752; 12414957; 12419805; 12482663; 12486136; 12502873; 12504564; 12525647; 12526811; 12574335; 12584329; 12682255; 12734410; 12746459; 12767938; 12788643; 12810958; 12816953; 12824470; 12836198; 12842621; 12853962; 12855553; 12884192; 12884293; 12960275; 12970439; 13679604; 14531802; 14557639; 14597672; 14617802; 14670336; 14691137; 14694087; 14737186; 14747534; 14759364; 14965316; 14990729; 15033985; 15047825; 15075535; 15078178; 15137387; 15140972; 15163745; 15166428; 15166429; 15186530; 15194762; 15202998; 15258149; 15262497; 15343382; 15371598; 15452229; 15459189; 15491611; 15494497; 15518810; 15556689; 15569681; 15569716; 15576488; 15595833; 15596859; 15611114; 15611225; 15613341; 15626739; 15629779; 15632291; 15637102; 15638726; 15653685; 15681409; 15722538; 15767427; 15827086; 15847608; 15854903; 15858021; 15878340; 15892963; 15916790; 15928037; 15942894; 15956605; 15976924; 16000390; 16014965; 16021629; 16043695; 16091223; 16103193; 16116206; 16177101; 16177107; 16179353; 16237100; 16253302; 16260903; 16272310; 16282498; 16310238; 16354571; 16356860; 16365153; 16374509; 16385629; 16429138; 16439540; 16445909; 16454711; 16475823; 16476977; 16501114; 16515720; 16684552; 16687395; 16730880; 16764724; 16775006; 16777597; 16847125; 16849330; 16857988; 16873261; 16877303; 16912329; 16916529; 16921384; 16928758; 16978607; 16979207; 16987968; 16988698; 17042973; 17046994; 17076584; 17077296; 17083721; 17086054; 17116886; 17140399; 17170457; 17182689; 17209762; 17261081; 17266559; 17267500; 17314161; 17329339; 17331028; 17346169; 17411376; 17411382; 17412836; 17431094; 17443671; 17547741; 17581864; 17586321; 17600593; 17630924; 17632197; 17632570; 17634131; 17652391; 17670831; 17707624; 17824250; 17878955; 17881449; 17893228; 17904606; 17920628; 17928336; 17947540; 17967742; 18003888; 18005680; 18005690; 18030346; 18032517; 18042718; 18057255; 18073204; 18089753; 18094167; 18155264; 18178851; 18187620; 18220834; 18234668; 18296443; 18322217; 18336259; 18337699; 18438604; 18443354; 18462992; 18473783; 18489774; 18523251; 18524831; 18539368; 18541215; 18555888; 18596106; 18621011; 18653452; 18707241; 18715908; 18725938; 18799583; 18808677; 18826950; 18854243; 18987145; 18991615; 19013323; 19050260; 19081837; 19091857; 19102781; 19129443; 19130504; 19146681; 19149577; 19150430; 19254361; 19263804; 19269660; 19324886; 19327048; 19403684; 19439470; 19449444; 19455469; 19540523; 19555986; 19585521; 19605470; 19615357; 19620308; 19635843; 19641037; 19643141; 19651874; 19683683; 19726522; 19748111; 19759518; 19770068; 19781555; 19807124; 19847956; 19859083; 19878567; 19895210; 19912576; 19917496; 19935658; 20012528; 20015995; 20020046; 20056088; 20068037; 20126615; 20147394; 20156100; 20179761; 20299515; 20367240; 20377428; 20380698; 20392440; 20444900; 20463068; 20465832; 20479131; 20488787; 20504918; 20530791; 20535218; 20566577; 20594957; 20598119; 20622010; 20638642; 20659345; 20667578; 20702582; 20731376; 20739067; 20810664; 20826747; 20881088; 20942936; 21044805; 21068258; 21093412; 21165790; 21176845; 21179446; 21209113; 21255447; 21292773; 21336563; 21347424; 21365684; 21394196; 21449607; 21459854; 21464919; 21477083; 21482738; 21504576; 21543478; 21555514; 21567396; 21606541; 21625496; 21642447; 21653836; 21668366; 21696586; 21738584; 21762823; 21763498; 21814282; 21819585; 21824805; 21845735; 21849975; 21858117; 21861776; 21886773; 21892329; 21896007; 21917951; 21922073; 21923909; 21970979; 21994772; 22013042; 22013062; 22066947; 22103831; 22103832; 22103833; 22103834; 22103836; 22103837; 22103838; 22110726; 22123847; 22171785; 22174682; 22175768; 22190034; 22190037; 22262807; 22291690; 22301137; 22301152; 22323535; 22345473; 22345475; 22393415; 22395607; 22407921; 22422068; 22479639; 22496420; 22534017; 22537596; 22553319; 22583022; 22613796; 22640559; 22643973; 22651890; 22655069; 22672539; 22705789; 22721673; 22767237; 22802418; 22808111; 22826228; 22844345; 22980332; 22980333; 23067370; 23071112; 23093676; 23151229; 23170180; 23185362; 23284715; 23417613; 23490051; 23678182; 23746211; 23799149; 23855121; 23899341; 24051604; 24489825
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].
1920
p27
Other designations: Nef
nef
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
811213
PFL0800c
20120919
36329
12
protein-coding
NCBI-supplied
PMID: 12368864
MUTATION: CelTOS mutant has reduced infectivity in rat liver and almost abolished its cell-passage ability [PMID:16468982].
1979
CelTOS, putative
CelTOS
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
812450
PFD0210c
20140406
36329
4
protein-coding
NCBI-supplied
PMID: 12368867; 16267556
MUTATION: pbs36 had arrested intracellular growth in liver HC-04 cells [PMID:19625622].
1978
pbs36 homologue
PFD0210c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
812616
PFB0100c
20140406
36329
2
protein-coding
NCBI-supplied
PMID: 9804551; 12368864; 16006556; 16267556; 16507777; 21594767; 21696460; 24090929
MUTATION: KAHRP mutant has reduced adherence to CD36 when tested under flow conditions that mimic those of postcapillary venules [PMID:9108483].
1977
knob-associated histidine-rich protein
PFB0100c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
814166
PF13_0197
20140406
36329
13
protein-coding
NCBI-supplied
GO_0016020 (EC: TAS, PMID: 11551634); GO_0030260 (EC: TAS, PMID: 11551634)
PMID: 11551634; 16267556; 16940297; 17944453; 20472690; 23049905
MUTATION: msp7 mutant is attenuated for invasion of erythrocytes compared to the wild type [PMID:18820076].
2018
Merozoite Surface Protein 7 precursor, MSP7
MSP7
Bin Zhao, Oliver He
SSP-2
SSP2
WEB: http://www.ncbi.nlm.nih.gov/gene
814170
PF13_0201
20140222
36329
13
protein-coding
NCBI-supplied
MUTATION: TRAP mutant is attenuated for sporozoite infection of rat liver [PMID:9267031].
2017
Thrombospondin-related anonymous protein, TRAP
-
TRAP
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
850342
YCL018W
20140406
559292
III
protein-coding
NCBI-supplied
GO_0000287 (EC: IEA); GO_0003862 (EC: IDA, PMID: 3071718); GO_0003862 (EC: IEA); GO_0003862 (EC: IMP, PMID: 6297759); GO_0005737 (EC: IEA); GO_0005829 (EC: IDA, PMID: 4355481); GO_0006097 (EC: IMP); GO_0008652 (EC: IEA); GO_0009082 (EC: IEA); GO_0009098 (EC: IEA); GO_0009098 (EC: IMP, PMID: 6297759); GO_0016491 (EC: IEA); GO_0016616 (EC: IEA); GO_0046872 (EC: IEA); GO_0051287 (EC: IEA); GO_0055114 (EC: IEA)
PMID: 1574125; 3071718; 4355481; 6297759; 8849441; 10409731; 11788966; 15292183; 16319894; 18071269; 18087042; 19270382; 21427232; 21441928; 21526172; 21825077; 21919885; 21926174; 23050233
MUTATION: leu2 mutant is attenuated in mice [PMID:11606528].
4821
3-isopropylmalate dehydrogenase
LEU2
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
854295
YOR128C
20140406
559292
XV
protein-coding
NCBI-supplied
GO_0000166 (EC: IEA); GO_0003824 (EC: IEA); GO_0004638 (EC: IEA); GO_0004638 (EC: IMP, PMID: 5767024); GO_0005524 (EC: IEA); GO_0005737 (EC: IDA, PMID: 14562095); GO_0006144 (EC: IMP, PMID: 8939809); GO_0006164 (EC: IC, PMID: 5767024); GO_0006164 (EC: IEA); GO_0006189 (EC: IC, PMID: 5767024); GO_0006189 (EC: IEA); GO_0016829 (EC: IEA); GO_0016831 (EC: IEA); GO_0034023 (EC: IEA); GO_0046872 (EC: IEA)
PMID: 5767024; 8849441; 8939809; 9169874; 9589850; 10688190; 10822807; 11283351; 14562095; 16554755; 16630557; 17720931; 17923092; 18087042; 18245832; 18762987; 19160453; 19840948; 20093466; 20170199; 21552543; 21623372; 22140548; 23209445; 23222640; 23793018; 23831759
MUTATION: ade2 mutant is attenuated in mice [PMID:11606528].
4818
phosphoribosylaminoimidazole carboxylase ADE2
ADE2
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
854508
YOR330C
20140406
559292
XV
protein-coding
NCBI-supplied
GO_0003676 (EC: IEA); GO_0003677 (EC: IEA); GO_0003887 (EC: IDA); GO_0003887 (EC: IEA); GO_0005739 (EC: IDA, PMID: 14576278); GO_0005739 (EC: IEA); GO_0005760 (EC: IEA); GO_0006260 (EC: IEA); GO_0006261 (EC: IEA); GO_0006264 (EC: IDA, PMID: 12023279); GO_0006264 (EC: IMP, PMID: 2684980); GO_0008408 (EC: IDA); GO_0016740 (EC: IEA); GO_0016779 (EC: IEA)
PMID: 2684980; 8552025; 8849441; 9169874; 9774971; 12023279; 14576278; 15351639; 16487579; 16940310; 17314980; 17720904; 17980715; 18676811; 19547744; 20185557; 20601675; 21987634; 22114710; 22199229; 22470557; 23589460
MUTATION: mip1 mutant is attenuated in mice [PMID:11606528].
4822
Mip1p
MIP1
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
856692
YEL021W
20140406
559292
V
protein-coding
NCBI-supplied
GO_0003824 (EC: IEA); GO_0004590 (EC: IDA, PMID: 2061334); GO_0004590 (EC: IEA); GO_0004590 (EC: IMP, PMID: 4550660); GO_0005829 (EC: IDA, PMID: 18812321); GO_0006207 (EC: IEA); GO_0006207 (EC: IMP, PMID: 4550660); GO_0006221 (EC: IEA); GO_0006222 (EC: IDA, PMID: 2061334); GO_0006222 (EC: IMP, PMID: 5651325); GO_0008152 (EC: IEA); GO_0016829 (EC: IEA); GO_0016831 (EC: IEA); GO_0044205 (EC: IEA)
PMID: 2061334; 4550660; 5651325; 8849441; 9169868; 9829833; 10207060; 10688190; 11805837; 12684846; 12872131; 15455074; 16554755; 18186026; 18812321; 19435314; 19618917; 19840948; 23276261; 23749301; 23793018
MUTATION: ura3 mutant is attenuated in mice [PMID:11606528].
4823
orotidine-5'-phosphate decarboxylase
URA3
MUTATION: mxiC mutant has a 10-fold decrease in efficiency in invading epithelial cells [PMID:19017268].
24
MUTATION: virF knockouts are non-invasive to host cells [PMID:20237205].
25
MUTATION: spa47 mutants form needle-less type III structure which is defective, and thus incapable of invasion of host cells [PMID:10921870].
26
MUTATION: spa15 mutant was attenuated in entry into epithelial cells compared to the wild-type [PMID:11952903].
27
MUTATION: transposon mutants of ipgA cannot invade epithelial cells and cannot induce keratoconjunctivitis in mice [PMID:8376337].
28
MUTATION: ipaD mutants are completely unable to invade cultured cells or lyse RBCs [PMID:15731041] .
29
MUTATION: ipgC mutant attenuated in infecting Caco-2 cells monolayer [PMID:11207551].
30
MUTATION: ipaC mutants cannot invade cultured cells or lyse red blood cells [PMID:18656530].
31
MUTATION: ipaB mutant is unable to infect HeLa cells [PMID:20086081].
32
MUTATION: spa33 mutants are unable to secrete effectors necessary to cell invasion [PMID:16246841].
33
MUTATION: virA mutants did not move within the host cytoplasm and failed to move into adjacent cells [PMID:17095701].
34
MUTATION: virG mutants are able to replicate in cells, but cell to cell spread is attenuated in monkey kidney epithelial cells [PMID:2644195].
35
MUTATION: transposon mutants of ipgB cannot invade epithelial cells and cannot induce keratoconjunctivitis in mice [PMID:8376337].
36
MUTATION: ipgD mutant is unable to dephosphorylate phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] and induces shorter filapodia in host cells [PMID:12356723].
37
MUTATION: mxiG mutant was unable to enter HeLa cells and to provoke keratoconjunctivitis in guinea-pigs [PMID:8559065].
38
MUTATION: spa32 mutants are unable to invade HeLa cells and do not secrete type III effectors [PMID:11844752].
39
MUTATION: mxiI mutant is unable to invade HeLa cells [PMID:11169106].
40
MUTATION: mxiM mutants are phenotypically avirulent, and also unable to invade semiconfluent L2 cell monolayers [PMID:10085046].
41
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].
42
MUTATION: mxiD mutant is unable to invade HeLa cells or to provoke keratoconjunctivitis in guinea-pigs [PMID:8437520].
43
MUTATION: mxiE deletion mutants are unable to block apoptosis of host epithelial cells [PMID:17339354].
44
MUTATION: mxiK mutants are unable to invade HeLa cells [PMID:12864857].
45
MUTATION: virB mutants have an avirulent phenotype and do not invade host cells [PMID:8385666].
46
MUTATION: mxiA mutants were attenuated in invasion of HeLa cells [PMID:2037361].
47
MUTATION: mxiD mutant is unable to invade HeLa cells or to provoke keratoconjunctivitis in guinea-pigs [PMID:8437520].
48
MUTATION: icsB mutants are attenuated in guinea pig eyes [PMID:12753186].
49
MUTATION: virK mutants have attenuated ability for intracellular spreading in host cells [PMID:15664968].
50
MUTATION: mxiH mutants are unable to invade HeLa cells [PMID:11169106].
51
MUTATION: ipaA mutants are attenuated in invasion of HeLa cells [PMID:9184218].
52
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].
53
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].
54
MUTATION: sepA mutant has attenuated virulence in ligated rabbit ileal loop model [PMID:7476198].
55
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].
56
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
877618
PA0584
20140322
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: cca mutant is attenuated in rats [PMID:14641575].
4201
multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase
cca
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
877661
PA1863
20140322
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: modA mutant is attenuated in rats [PMID:14641575].
4202
molybdate-binding periplasmic protein ModA
modA
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
877662
PA1927
20140405
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: metE mutant is attenuated in rats [PMID:14641575].
4203
5-methyltetrahydropteroyltriglutamate/homocysteine S-methyltransferase
metE
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
877674
PA5261
20140405
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 17766417; 18178737; 18978025; 19270096; 24097945
MUTATION: algR mutant is attenuated in mice [PMID:12379685].
4204
alginate biosynthesis regulatory protein AlgR
algR
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
877847
PA5441
20120929
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18083816; 18978025
MUTATION: PA5441 mutant is attenuated in rats [PMID:14641575].
4205
hypothetical protein
PA5441
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
877850
PA1148
20140406
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025; 19686346; 21945328; 22013118; 22520464; 22844393; 24605680
exotoxin A
toxA
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
877859
PA4554
20140406
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: pilY1 mutant is attenuated in rats [PMID:14641575].
4207
type 4 fimbrial biogenesis protein PilY1
pilY1
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
877861
PA4528
20140322
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: pilD mutant is attenuated in rats [PMID:14641575].
4208
type 4 prepilin peptidase PilD
pilD
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
877878
PA5437
20140222
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18599838; 18978025
MUTATION: PA5437 mutant is attenuated in rats [PMID:14641575].
4209
transcriptional regulator
PA5437
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
877893
PA0151
20130511
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: PA0151 mutant is attenuated in rats [PMID:14641575].
4210
TonB-dependent receptor
PA0151
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
877954
PA0765
20140322
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: mucC mutant is attenuated in rats [PMID:14641575].
4211
positive regulator for alginate biosynthesis MucC
mucC
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
877979
PA5312
20140315
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: PA5312 mutant is attenuated in rats [PMID:14641575].
4212
aldehyde dehydrogenase
PA5312
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
878014
PA5449
20131030
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: wbpX mutant is attenuated in rats [PMID:14641575].
4213
glycosyltransferase WbpX
wbpX
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
878015
PA4944
20140322
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 16468994; 17015649; 18978025; 21169425; 23897473
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].
4214
RNA-binding protein Hfq
hfq
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
878134
PA5131
20140405
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: pgm mutant is attenuated in rats [PMID:14641575].
4215
phosphoglyceromutase
pgm
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
878186
PA0410
20140322
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: pilI mutant is attenuated in rats [PMID:14641575].
4216
twitching motility protein PilI
pilI
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
878236
PA4855
20140405
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: purD mutant is attenuated in rats [PMID:14641575].
4217
phosphoribosylamine--glycine ligase
purD
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
878250
PA5327
20130511
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: PA5327 mutant is attenuated in rats [PMID:14641575].
4218
oxidoreductase
PA5327
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
878350
PA0044
20140222
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15731071; 15908409; 15995206; 16030221; 17015649; 18053004; 18978025; 22250085
exoenzyme T
exoT
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
878396
PA0073
20140215
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: PA0073 mutant is attenuated in rats [PMID:14641575].
4220
ABC transporter ATP-binding protein
PA0073
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
878601
PA0041
20140215
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: PA0041 mutant is attenuated in rats [PMID:14641575].
4221
hemagglutinin
PA0041
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
878826
PA5112
20140322
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 17631636; 18978025
MUTATION: estA mutant is attenuated in rats [PMID:14641575].
4222
esterase
estA
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
878954
PA3478
20140215
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: rhlB mutant is attenuated in rats [PMID:14641575].
4223
rhamnosyltransferase subunit B
rhlB
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
879028
PA1157
20140406
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: PA1157 mutant is attenuated in rats [PMID:14641575].
4224
two-component response regulator
PA1157
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
879198
PA0552
20140405
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: pgk mutant is attenuated in rats [PMID:14641575].
4225
phosphoglycerate kinase
pgk
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
879264
PA1009
20140222
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: PA1009 mutant is attenuated in rats [PMID:14641575].
4226
hypothetical protein
PA1009
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
879357
PA0763
20140215
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025; 19168621; 19298369; 20045914; 20174684; 21194804; 21631603; 22842599; 23068105
MUTATION: mucA mutant is attenuated in wounded alfalfa seedling infection model [PMID:12426404].
4227
anti-sigma factor MucA
mucA
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
879402
PA0082
20140222
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: PA0082 mutant is attenuated in rats [PMID:12023080].
4228
hypothetical protein
PA0082
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
879406
PA5322
20140406
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 16880541; 17015649; 18978025; 19253818
MUTATION: algC mutant is attenuated in neonatal mouse model of infection [PMID:8557368].
4229
phosphomannomutase
algC
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
879421
PA2191
20140222
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15192021; 15608211; 15716452; 15731071; 15908409; 15995206; 16030221; 16039071; 17015649; 18978025; 21843628
adenylate cyclase
exoY
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
879553
PA0090
20140322
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: clpV1 mutant is attenuated in rats [PMID:14641575].
4231
ClpV1 protein
clpV1
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
879629
PA5078
20140215
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: mdoG mutant is attenuated in rats [PMID:14641575].
4232
glucan biosynthesis protein G
PA5078
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
879752
PA3763
20140405
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: purL mutant is attenuated in rats [PMID:14641575].
4233
phosphoribosylformylglycinamidine synthase
purL
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
879777
PA4115
20140215
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025; 20855735
MUTATION: PA4115 mutant is attenuated in rats [PMID:14641575].
4234
hypothetical protein
PA4115
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
879781
PA3876
20140222
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 16391109; 17015649; 18978025
MUTATION: narK2 mutant is attenuated in rats [PMID:14641575].
4235
nitrite extrusion protein 2
narK2
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
879799
PA2972
20140322
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: PA2972 mutant is attenuated in rats [PMID:14641575].
4236
Maf-like protein
PA2972
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
879837
PA3841
20140406
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15668029; 15716452; 15731071; 15901720; 15908409; 15995206; 16030221; 17015649; 17490406; 18039770; 18978025; 20144150; 20732998; 20805335; 22080193; 22250085; 23428533
MUTATION: exoS mutant is attenuated in a silk worm oral infection model [PMID:20805335].
4237
exoenzyme S
exoS
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
879865
PA3831
20140406
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: pepA mutant is attenuated in rats [PMID:14641575].
4238
leucyl aminopeptidase
pepA
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
879871
PA3826
20140215
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: PA3826 mutant is attenuated in rats [PMID:14641575].
4239
hypothetical protein
PA3826
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
879922
PA3160
20140222
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: wzz (wzz1) mutant is attenuated in mouse pneumonia model of infection [PMID:18065548].
4240
O-antigen chain length regulator
wzz
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
879968
PA2023
20140405
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: galU mutant is attenuated in corneal mouse model of infection [PMID:15213167].
4241
UTP-glucose-1-phosphate uridylyltransferase
galU
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
880024
PA3498
20140222
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: PA3498 mutant is attenuated in rats [PMID:14641575].
4242
oxidoreductase
PA3498
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
880046
PA4854
20140329
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: purH mutant is attenuated in rats [PMID:14641575].
4243
bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase
purH
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
880205
PA2998
20140322
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: ngrB mutant is attenuated in rats [PMID:14641575].
4244
Na(+)-translocating NADH-quinone reductase subunit B
nqrB
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
880314
PA3756
20130420
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: PA3756 mutant is attenuated in rats [PMID:14641575].
4245
hypothetical protein
PA3756
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
880336
PA3735
20140406
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: thrC mutant is attenuated in rats [PMID:14641575].
4246
threonine synthase
thrC
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
880414
PA3001
20140405
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: PA3001 mutant is attenuated in rats [PMID:14641575].
4247
glyceraldehyde-3-phosphate dehydrogenase
PA3001
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
880514
PA4209
20140322
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 16946471; 17015649; 18292577; 18978025; 22562990
MUTATION: phzM mutant is attenuated in mice [PMID:15213173].
4248
phenazine-specific methyltransferase
phzM
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
880908
PA4564
20140222
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: PA4564 mutant is attenuated in rats [PMID:14641575].
4249
hypothetical protein
PA4564
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
880976
PA4446
20140322
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025; 19168621; 19298369
MUTATION: algW mutant is attenuated in rats [PMID:14641575].
4250
AlgW protein
algW
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
881054
PA4491
20140406
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: PA4491 mutant is attenuated in rats [PMID:14641575].
4251
hypothetical protein
PA4491
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
881072
PA4489
20140217
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025; 23919994
MUTATION: PA4489 mutant is attenuated in rats [PMID:14641575].
4252
hypothetical protein
PA4489
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
881219
PA4488
20140322
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: PA4488 mutant is attenuated in rats [PMID:14641575].
4253
hypothetical protein
PA4488
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
881227
PA1248
20140322
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: aprF mutant is attenuated in rats [PMID:14641575].
4254
alkaline protease secretion outer membrane protein AprF
aprF
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
881299
PA0934
20140406
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025; 22982211
MUTATION: relA mutant is attenuated in D. melanogaster [PMID:15385461].
4255
GTP pyrophosphokinase
relA
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
881475
PA4692
20140215
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: PA4692 mutant is attenuated in rats [PMID:14641575].
4256
sulfite oxidase subunit YedY
PA4692
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
881780
PA4764
20140322
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025; 23180123
MUTATION: fur mutant is attenuated in mouse corneal scratch model [PMID:7642283].
4257
ferric uptake regulation protein
fur
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
881789
PA1430
20140322
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15505212; 15608211; 15686549; 15716452; 15817780; 15908409; 15995202; 15995206; 16030221; 17015649; 17367209; 17449616; 17493132; 17559399; 18408026; 18978025; 19246742; 19682264; 21325039; 21415115; 21614486
MUTATION: lasR mutant is attenuated in neonatal mouse model of infection [PMID:8557368].
4258
transcriptional regulator LasR
lasR
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
881836
PA4217
20140215
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: phzS mutant is attenuated in mice [PMID:15213173].
4259
hypothetical protein
phzS
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
881933
PA1596
20140222
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: htpG mutant is attenuated in rats [PMID:12023080].
4260
heat shock protein 90
htpG
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
882052
PA1092
20140329
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15494517; 15608211; 15716452; 15908409; 15995206; 16030221; 16410345; 17015649; 18978025; 21205009
MUTATION: fliC mutant is attenuated in mice [PMID:9423837].
4261
flagellin type B
fliC
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
882125
PA0762
20140322
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025; 19226327; 20236169; 20348252; 22088575; 22842599
MUTATION: algU mutant is attenuated in rats [PMID:14641575].
4262
RNA polymerase sigma factor AlgU
algU
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
882140
PA0158
20140222
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: PA0158 mutant is attenuated in rats [PMID:12023080].
4263
resistance-nodulation-cell division (RND) efflux transporter
PA0158
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
882278
PA4887
20140406
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: PA4887 mutant is attenuated in rats [PMID:14641575].
4264
major facilitator superfamily (MFS) transporter
PA4887
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
882346
PA2639
20140405
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: nuoD mutant is attenuated in rats [PMID:14641575].
4265
bifunctional NADH:ubiquinone oxidoreductase subunit C/D
nuoD
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
882449
PA3286
20140222
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: PA3286 mutant is attenuated in rats [PMID:14641575].
4266
3-oxoacyl-ACP synthase
PA3286
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
882585
PA2876
20140329
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: pyrF mutant is attenuated in rats [PMID:14641575].
4267
orotidine 5'-phosphate decarboxylase
pyrF
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
882601
PA2895
20120929
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: PA2895 mutant is attenuated in rats [PMID:14641575].
4268
hypothetical protein
PA2895
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
882633
PA3173
20140215
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18978025
MUTATION: PA3173 mutant is attenuated in rats [PMID:14641575].
4269
short-chain dehydrogenase
PA3173
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
882839
PA2426
20140322
208964
protein-coding
NCBI-supplied
PMID: 10984043; 12644476; 12644477; 15608211; 15716452; 15908409; 15995206; 16030221; 17015649; 18047579; 18048935; 18502853; 18978025; 20370820; 21840975
MUTATION: pvdS mutant is attenuated in rabbit aortic endocarditis model [PMID:10720526].
4270
extracytoplasmic-function sigma-70 factor
pvdS
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
883600
RP819
20140301
272947
protein-coding
NCBI-supplied
PMID: 9823893; 19506016
MUTATION: pld mutant is attenuated in guinea pigs [PMID:19506016].
1451
hypothetical protein
RP819
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
884125
CT_135
20140322
272561
protein-coding
NCBI-supplied
PMID: 9784136
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].
4456
hypothetical protein
CT_135
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
884147
CT_119
20140322
272561
protein-coding
NCBI-supplied
PMID: 9784136; 15316015
MUTATION: IncA mutant showed decreased growth rate and infection in mice [PMID:18852248].
4457
Inclusion Membrane Protein A
incA
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885038
Rv0981
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 16513743; 17379732; 17601788; 20980199; 21821774; 22689819; 24187094
MUTATION: mprA mutant is attenuated in mice [PMID:11675502].
82
Mycobacterial persistence regulator MRPA (two component response transcriptional regulatory protein)
mprA
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885039
Rv3663c
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
83
Probable dipeptide-transport ATP-binding protein ABC transporter DppD
dppD
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885072
Rv1807
20140301
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
84
PPE family protein PPE31
PPE31
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885108
Rv1661
20131207
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: pks7 mutant is attenuated in mice [PMID:12855735].
85
Probable polyketide synthase Pks7
pks7
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885112
Rv1660
20140215
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: pks10 mutant is attenuated in mice [PMID:12730158].
86
Chalcone synthase Pks10
pks10
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885116
Rv1710
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 18084093; 18300244; 20980199
MUTATION: attenuated in mice [PMID:14569030].
87
Possible segregation and condensation protein ScpB
scpB
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885120
Rv1092c
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 16508093; 16699190; 19307712; 20451532; 20576686; 20980199; 23661699
MUTATION: attenuated in mice [PMID:14569030].
88
Probable pantothenate kinase CoaA (pantothenic acid kinase)
coaA
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885125
Rv1653
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20184895; 20980199
MUTATION: attenuated in mice [PMID:14569030].
89
Probable glutamate N-acetyltransferase ArgJ
argJ
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885209
Rv0903c
20140215
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 16434396; 20980199; 22081401
MUTATION: prrA mutant is attenuated in murine macrophages [PMID:11953357].
90
Two component response transcriptional regulatory protein PrrA
prrA
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885250
Rv2392
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 16553880; 20980199
MUTATION: cysH mutants are attenuated in mice [PMID:16553880].
91
Probable 3'-phosphoadenosine 5'-phosphosulfate reductase CysH (PAPS reductase, thioredoxin DEP.) (padops reductase) (3'-phosphoadenylylsulfate reductase) (PAPS sulfotransferase)
cysH
Bin Zhao, Oliver He
ompATb
WEB: http://www.ncbi.nlm.nih.gov/gene
885286
Rv0899
20140215
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 17573469; 20199110; 20980199; 21117233; 21410778; 21802366; 22108166
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].
92
Outer membrane protein A OmpA
-
ompA
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885296
Rv3651
20131207
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
93
hypothetical protein
Rv3651
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885300
Rv2388c
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
94
Probable oxygen-independent coproporphyrinogen III oxidase HemN (coproporphyrinogenase) (coprogen oxidase)
hemN
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885302
Rv2387
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
95
hypothetical protein
Rv2387
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885311
Rv1747
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199; 21622570
MUTATION: Rv1747 mutant is attenuated in mice [PMID:16040957].
96
Probable conserved transmembrane ATP-binding protein ABC transporter
Rv1747
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885314
Rv3631
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
97
Possible transferase (possibly glycosyltransferase)
Rv3631
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885344
Rv1930c
20131130
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
98
hypothetical protein
Rv1930c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885364
Rv0986
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: Rv0986 mutant is attenuated in survival within macrophages [PMID:15340136].
99
Probable adhesion component transport ATP-binding protein ABC transporter
Rv0986
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885377
Rv3616c
20140125
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199; 24078612
MUTATION: Rv3616c mutant is attenuated in mice [PMID:16030141].
100
ESX-1 secretion-associated protein A, EspA
espA
Bin Zhao, Oliver He
mtb32b
WEB: http://www.ncbi.nlm.nih.gov/gene
885382
Rv0983
20140215
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199; 21445360
MUTATION: pepD mutant has altered virulence in mouse model of infection [PMID:20061478].
101
Probable serine protease PepD (serine proteinase) (MTB32B)
-
pepD
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885428
Rv1640c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
102
Lysyl-tRNA synthetase 2 LysX
lysX
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885437
Rv1931c
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
103
Probable transcriptional regulatory protein
Rv1931c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885438
Rv0950c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
104
hypothetical protein
Rv0950c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885439
Rv1811
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: mgtC mutant is attenuated in human macrophages and mice [PMID:10760138].
105
Possible Mg2+ transport P-type ATPase C MgtC
mgtC
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885447
Rv1111c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
106
hypothetical protein
Rv1111c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885459
Rv3602c
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: panCD mutant is attenuated in mice [PMID:12219086].
107
Pantoate--beta-alanine ligase PanC (pantothenate synthetase) (pantoate activating enzyme)
panC
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885472
Rv2391
20140329
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 15917234; 20980199
MUTATION: attenuated in mice [PMID:14569030].
108
Ferredoxin-dependent sulfite reductase SirA
sirA
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885488
Rv1939
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
109
Probable oxidoreductase
Rv1939
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885502
Rv3676
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 15882420; 16267303; 16946467; 17702648; 19193643; 19740754; 20028978; 20980199; 21902733
MUTATION: Rv3676 mutant is attenuated in human macrophages and mice [PMID:15882420].
110
Transcriptional regulatory protein Crp (Crp/Fnr-family)
crp
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885521
Rv3701c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
111
hypothetical protein
Rv3701c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885594
Rv1821
20140329
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 17030572; 18487341; 19240020; 20980199; 24297168
MUTATION: secA2 mutant is attenuated in mice [PMID:12675804].
112
Possible preprotein translocase ATPase SecA2
secA2
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885596
Rv3601c
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: panCD mutant is attenuated in mice [PMID:12219086].
113
Probable aspartate 1-decarboxylase precursor PanD (aspartate alpha-decarboxylase)
panD
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885602
Rv3717
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199; 24019530
MUTATION: attenuated in mice [PMID:14569030].
114
hypothetical protein
Rv3717
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885638
Rv1908c
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 15498158; 15628865; 15840564; 16285713; 16566587; 17204474; 17260948; 17309235; 17539290; 17978919; 18394163; 19050300; 19139098; 19139099; 19334480; 19741059; 19750330; 20054829; 20211896; 20980199; 21244531; 21388297; 21554227; 22272299; 22358357; 22381358; 22610803; 22808802; 22918833; 23325741; 23412028; 23453008
MUTATION: katG mutant is attenuated in mice and guinea pigs [PMID:9534978].
115
Catalase-peroxidase-peroxynitritase T KatG
katG from M. tuberculosis H37Rv
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885717
Rv2428
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 15498158; 15886207; 20980199
MUTATION: ahpC mutant has decreased survival in unstimulated macrophages compared to the wild type [PMID:12368447].
116
Alkyl hydroperoxide reductase C protein AhpC (alkyl hydroperoxidase C)
ahpC
Bin Zhao, Oliver He
snm9
WEB: http://www.ncbi.nlm.nih.gov/gene
885770
Rv3615c
20140217
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 16135231; 20980199
MUTATION: Rv3615c mutant is attenuated in mice and has growth defects in macrophages [PMID:16135231].
117
ESX-1 secretion-associated protein EspC
-
espC
Bin Zhao, Oliver He
snm10
WEB: http://www.ncbi.nlm.nih.gov/gene
885777
Rv3614c
20131207
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 16135231; 20980199
MUTATION: Rv3614c mutant is attenuated in mice and has growth defects in macrophages [PMID:16135231].
118
ESX-1 secretion-associated protein EspD
-
espD
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885780
Rv3683
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
119
hypothetical protein
Rv3683
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885791
Rv3723
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
120
Probable conserved transmembrane protein
Rv3723
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885805
Rv1696
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
121
Probable DNA repair protein RecN (recombination protein N)
recN
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885814
Rv1524
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
122
Probable glycosyltransferase
Rv1524
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885828
Rv1109c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
123
hypothetical protein
Rv1109c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885838
Rv2383c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199; 22447909
MUTATION: mbtB mutant is attenuated in macrophage like THP-1 cells [PMID:10655517].
124
Phenyloxazoline synthase MbtB (phenyloxazoline synthetase)
mbtB
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885841
Rv3649
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
125
Probable helicase
Rv3649
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885849
Rv1128c
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
126
hypothetical protein
Rv1128c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885861
Rv1099c
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199; 21636919
MUTATION: attenuated in mice [PMID:14569030].
127
Fructose 1,6-bisphosphatase GlpX
glpX
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885906
Rv2437
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
128
Conserved transmembrane protein
Rv2437
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885924
Rv2374c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
129
Probable heat shock protein transcriptional repressor HrcA
hrcA
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885929
Rv0353
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 18227252; 20980199; 22753065
MUTATION: hspR is attenuated in mice [PMID:11385512].
130
Probable heat shock protein transcriptional repressor HspR (MerR family)
hspR
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885932
Rv1144
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
131
Probable short-chain type dehydrogenase/reductase
Rv1144
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
885935
Rv1974
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
132
Probable conserved membrane protein
Rv1974
Bin Zhao, Oliver He
mce3
WEB: http://www.ncbi.nlm.nih.gov/gene
885944
Rv1966
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 15804490; 18201981; 20980199
MUTATION: mce3A mutant is attenuated in mice [PMID:15804490].
133
Mce-family protein Mce3A
-
mce3A
Bin Zhao, Oliver He
mpcA
WEB: http://www.ncbi.nlm.nih.gov/gene
885995
Rv2351c
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: plcABC triple mutants are attenuated in mice [PMID:12100560].
134
Membrane-associated phospholipase C 1 PlcA (MTP40 antigen)
-
plcA
Bin Zhao, Oliver He
mpcB
WEB: http://www.ncbi.nlm.nih.gov/gene
885999
Rv2350c
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: plcABC triple mutants are attenuated in mice [PMID:12100560].
135
Membrane-associated phospholipase C 2 PlcB
-
plcB
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886000
Rv2349c
20140329
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: plcABC triple mutants are attenuated in mice [PMID:12100560].
136
Probable phospholipase C 3 PlcC
plcC
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886007
Rv1192
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
137
hypothetical protein
Rv1192
Bin Zhao, Oliver He
furB
WEB: http://www.ncbi.nlm.nih.gov/gene
886009
Rv2359
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 17098899; 17213192; 18452427; 20980199
MUTATION: attenuated in mice [PMID:14569030].
138
Probable zinc uptake regulation protein Zur
-
zur
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886012
Rv2335
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199; 23483228
MUTATION: attenuated in mice [PMID:14569030].
139
Probable serine acetyltransferase CysE (sat)
cysE
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886030
Rv0386
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 15955067; 20980199
MUTATION: Rv0386 mutant is attenuated in mice [PMID:20039878].
140
Probable transcriptional regulatory protein (probably LuxR/UhpA-family)
Rv0386
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886035
Rv1013
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
141
Putative polyketide synthase Pks16
pks16
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886052
Rv1021
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20529853; 20980199
MUTATION: attenuated in mice [PMID:14569030].
142
hypothetical protein
Rv1021
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886063
Rv1184c
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
143
Possible exported protein
Rv1184c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886065
Rv1185c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
144
Probable fatty-acid-AMP ligase FadD21 (fatty-acid-AMP synthetase) (fatty-acid-AMP synthase)
fadD21
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886066
Rv1016c
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
145
Probable conserved lipoprotein LpqT
lpqT
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886068
Rv1183
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
146
Probable conserved transmembrane transport protein MmpL10
mmpL10
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886084
Rv1028c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 12581360; 20980199
MUTATION: attenuated in mice [PMID:14569030].
147
Probable sensor protein KdpD
kdpD
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886113
Rv3781
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
148
Probable O-antigen/lipopolysaccharide transport ATP-binding protein ABC transporter RfbE
rfbE
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886123
Rv3794
20131207
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 16585755; 18174142; 20980199
MUTATION: attenuated in mice [PMID:14569030].
149
Integral membrane indolylacetylinositol arabinosyltransferase EmbA (arabinosylindolylacetylinositol synthase)
embA
Bin Zhao, Oliver He
85A
mpt44
WEB: http://www.ncbi.nlm.nih.gov/gene
886132
Rv3804c
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 17357846; 19959397; 20375425; 20980199; 21819455
MUTATION: fbpA mutant is attenuated in mice [PMID:15557632].
150
Secreted antigen 85-a FbpA (mycolyl transferase 85A) (fibronectin-binding protein A) (antigen 85 complex A)
-
fbpA
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886138
Rv3805c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
151
Possible arabinofuranosyltransferase AftB
aftB
Bin Zhao, Oliver He
P36
erp
WEB: http://www.ncbi.nlm.nih.gov/gene
886139
Rv3810
20131130
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
152
Exported repetitive protein precursor PirG (cell surface protein) (EXP53)
-
pirG
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886145
Rv3823c
20140217
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: mmpL8 mutant is attenuated in mice [PMID:12724526].
153
Conserved integral membrane transport protein MmpL8
mmpL8
Bin Zhao, Oliver He
snm6
WEB: http://www.ncbi.nlm.nih.gov/gene
886166
Rv3869
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
154
ESX conserved component EccB1 ESX-1 type VII secretion system protein Possible membrane protein
-
eccB1
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886172
Rv3865
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: Rv3865 mutant is attenuated in mice [PMID:16368961].
155
ESX-1 secretion-associated protein EspF
espF
Bin Zhao, Oliver He
sod
sodB
WEB: http://www.ncbi.nlm.nih.gov/gene
886174
Rv3846
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: sodA mutant is attenuated in mice [PMID:11751190].
156
Superoxide dismutase [FE] SodA
-
sodA
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886185
Rv3864
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
157
ESX-1 secretion-associated protein EspE
espE
Bin Zhao, Oliver He
aka
etaR
WEB: http://www.ncbi.nlm.nih.gov/gene
886189
Rv3855
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199; 22156370
MUTATION: attenuated in mice [PMID:14569030].
158
Transcriptional regulatory repressor protein (TetR-family) EthR
-
ethR
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886191
Rv3872
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
159
PE family-related protein PE35
PE35
Bin Zhao, Oliver He
cfp10
lhp
WEB: http://www.ncbi.nlm.nih.gov/gene
886194
Rv3874
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 15378760; 15973432; 16689931; 16785544; 16973880; 17676952; 19682254; 19854905; 20980199; 22723257; 23308124; 24078612
MUTATION: esxB (CFP-10) mutant is attenuated in mice [PMID:16030141].
160
10 kDa culture filtrate antigen EsxB (LHP) (CFP10)
-
esxB
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886199
Rv3868
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 17676952; 19682254; 20980199
MUTATION: attenuated in mice [PMID:14569030].
161
ESX conserved component EccA1 ESX-1 type VII secretion system protein
eccA1
Bin Zhao, Oliver He
snm5
WEB: http://www.ncbi.nlm.nih.gov/gene
886200
Rv3866
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 17676952; 20980199
MUTATION: Rv3866 mutant is attenuated in mice [PMID:16368961].
162
ESX-1 secretion-associated protein EspG1
-
espG1
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886201
Rv3873
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 18686610; 20980199
MUTATION: attenuated in mice [PMID:14569030].
163
PPE family protein PPE68
PPE68
Bin Zhao, Oliver He
snm2
WEB: http://www.ncbi.nlm.nih.gov/gene
886202
Rv3871
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 17676952; 20034878; 20980199; 22723257
MUTATION: Rv3871 mutant is attenuated in mice [PMID:14557536].
164
ESX conserved component EccCb1 ESX-1 type VII secretion system protein
-
eccCb1
Bin Zhao, Oliver He
snm1
WEB: http://www.ncbi.nlm.nih.gov/gene
886204
Rv3870
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 17676952; 20980199
MUTATION: Rv3870 mutant is attenuated in mice [PMID:14557536].
165
ESX conserved component EccCa1 ESX-1 type VII secretion system protein Possible transmembrane protein
-
eccCa1
Bin Zhao, Oliver He
snm3
WEB: http://www.ncbi.nlm.nih.gov/gene
886206
Rv3876
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 17676952; 20980199
MUTATION: attenuated in mice [PMID:14569030].
166
ESX-1 secretion-associated protein EspI Conserved proline and alanine rich protein
-
espI
Bin Zhao, Oliver He
snm4
WEB: http://www.ncbi.nlm.nih.gov/gene
886207
Rv3877
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 17676952; 20980199
MUTATION: Rv3877 (snm4) mutant is attenuated in mice [PMID:14557536].
167
ESX conserved component EccD1 ESX-1 type VII secretion system protein Probable transmembrane protein
-
eccD1
Bin Zhao, Oliver He
snm7
WEB: http://www.ncbi.nlm.nih.gov/gene
886208
Rv3882c
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
168
ESX conserved component EccE1 ESX-1 type VII secretion system protein Possible membrane protein
-
eccE1
Bin Zhao, Oliver He
esat-6
WEB: http://www.ncbi.nlm.nih.gov/gene
886209
Rv3875
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 15488391; 15860216; 15973432; 16368961; 17298391; 17486091; 17676952; 17915024; 18779346; 19265145; 19340290; 19854905; 19901982; 19906174; 20006311; 20007864; 20148899; 20617139; 20980199; 21039742; 21586573; 21637850; 21689705; 22712528; 22808273; 23150662; 23308124; 24078612
MUTATION: esxA (ESAT-6) mutant is attenuated in mice [PMID:16030141].
169
6 kDa early secretory antigenic target EsxA (ESAT-6)
-
esxA
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886211
Rv3887c
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: Rv3887c mutant is attenuated in mice [PMID:17353284].
170
ESX conserved component EccD2 ESX-2 type VII secretion system protein Probable transmembrane protein
eccD2
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886214
Rv3881c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 17676952; 20980199
MUTATION: Rv3881c (espB) mutant is attenuated in macrophages [PMID:17676952].
171
Secreted ESX-1 substrate protein B, EspB. Conserved alanine and glycine rich protein
espB
Bin Zhao, Oliver He
snm8
WEB: http://www.ncbi.nlm.nih.gov/gene
886217
Rv3883c
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20227664; 20980199
MUTATION: mycP1 mutant is attenuated in chronic infection of mice [PMID:20227664].
172
Membrane-anchored mycosin MycP1 (serine protease) (subtilisin-like protease) (subtilase-like) (mycosin-1)
-
mycP1
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886247
Rv3910
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
173
Probable conserved transmembrane protein
Rv3910
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886272
Rv0475
20131207
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 15973422; 16893986; 17933894; 18441065; 20178790; 20980199; 21398546; 21672524; 22174691; 22306117; 22403657
MUTATION: hbhA mutant is attenuated in attachment and invasion of pneumocytes [PMID:11449276].
174
Iron-regulated heparin binding hemagglutinin HbhA (adhesin)
hbhA
Bin Zhao, Oliver He
umaA2
WEB: http://www.ncbi.nlm.nih.gov/gene
886284
Rv0470c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199; 22621931
MUTATION: pcaA mutant is attenuated in mice [PMID:10882107].
175
Mycolic acid synthase PcaA (cyclopropane synthase)
-
pcaA
Bin Zhao, Oliver He
aceA
icl
WEB: http://www.ncbi.nlm.nih.gov/gene
886291
Rv0467
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 16879647; 18275086; 19767422; 20980199; 21814509
MUTATION: icl mutant is attenuated in activated macrophages [PMID:10963599].
176
Isocitrate lyase Icl (isocitrase) (isocitratase)
-
icl1
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886292
Rv1590
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
177
hypothetical protein
Rv1590
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886293
Rv3758c
20131207
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 18390665; 20980199
MUTATION: attenuated in mice [PMID:14569030].
178
Possible osmoprotectant (glycine betaine/carnitine/choline/L-proline) transport ATP-binding protein ABC transporter ProV
proV
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886301
Rv1589
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
179
Probable biotin synthetase BioB
bioB
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886343
Rv1568
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 16754301; 20565114; 20980199
MUTATION: attenuated in mice [PMID:14569030].
180
Adenosylmethionine-8-amino-7-oxononanoate aminotransferase BioA
bioA
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886345
Rv1569
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
181
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)
bioF1
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886358
Rv0432
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: sodC mutant is more susceptible to killing by activated murine macrophages than the wild type [PMID:11447176].
182
Periplasmic superoxide dismutase [Cu-Zn] SodC
sodC
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886359
Rv1560
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
183
Possible antitoxin VapB11
vapB11
Bin Zhao, Oliver He
xth
WEB: http://www.ncbi.nlm.nih.gov/gene
886370
Rv0427c
20140215
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
184
Probable exodeoxyribonuclease III protein XthA (exonuclease III) (EXO III) (AP endonuclease VI)
-
xthA
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886391
Rv0414c
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
185
Thiamine-phosphate pyrophosphorylase ThiE (TMP pyrophosphorylase) (TMP-PPASE) (thiamine-phosphate synthase)
thiE
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886397
Rv0410c
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 15155913; 17616581; 17641049; 19447903; 20030858; 20980199
MUTATION: pknG mutant is attenuated in mice [PMID:15186418].
186
Serine/threonine-protein kinase PknG (protein kinase G) (STPK G)
pknG
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886408
Rv1539
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 18832305; 20980199
MUTATION: lspA mutant is attenuated in mice [PMID:18832305].
187
Probable lipoprotein signal peptidase LspA
lspA
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886442
Rv1527c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: pks5 mutant is attenuated in mice [PMID:12855735].
188
Probable polyketide synthase Pks5
pks5
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886457
Rv1514c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
189
hypothetical protein
Rv1514c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886544
Rv0326
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
190
Hypothetical protein
Rv0326
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886569
Rv1465
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
191
Possible nitrogen fixation related protein
Rv1465
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886573
Rv1460
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
192
Probable transcriptional regulatory protein
Rv1460
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886578
Rv1469
20131207
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
193
Probable cation transporter P-type ATPase D CtpD
ctpD
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886670
Rv1422
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
194
hypothetical protein
Rv1422
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886671
Rv0249c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
195
Probable succinate dehydrogenase [membrane anchor subunit] (succinic dehydrogenase)
Rv0249c
Bin Zhao, Oliver He
P27
WEB: http://www.ncbi.nlm.nih.gov/gene
886700
Rv1411c
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 16815070; 20980199
MUTATION: attenuated in mice [PMID:14569030].
196
Conserved lipoprotein LprG
-
lprG
Bin Zhao, Oliver He
P55
WEB: http://www.ncbi.nlm.nih.gov/gene
886709
Rv1410c
20140215
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 19564371; 20980199
MUTATION: attenuated in mice [PMID:14569030].
197
Aminoglycosides/tetracycline-transport integral membrane protein
-
Rv1410c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886714
Rv1405c
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
198
Putative methyltransferase
Rv1405c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886727
Rv0218
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
199
Probable conserved transmembrane protein
Rv0218
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886729
Rv0216
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
200
Double hotdog hydratase
Rv0216
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886747
Rv0204c
20140215
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
201
Probable conserved transmembrane protein
Rv0204c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886750
Rv0202c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199; 23760277
MUTATION: mmpL11 mutant is attenuated in mice [PMID:15908378].
202
Probable conserved transmembrane transport protein MmpL11
mmpL11
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886753
Rv0199
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
203
Probable conserved membrane protein
Rv0199
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886799
Rv0176
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
204
Probable conserved Mce associated transmembrane protein
Rv0176
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886800
Rv1371
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
205
Probable conserved membrane protein
Rv1371
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886801
Rv0175
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
206
Probable conserved Mce associated membrane protein
Rv0175
Bin Zhao, Oliver He
mce1E
WEB: http://www.ncbi.nlm.nih.gov/gene
886804
Rv0173
20131207
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
207
Possible Mce-family lipoprotein LprK (Mce-family lipoprotein Mce1E)
-
lprK
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886808
Rv0171
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
208
Mce-family protein Mce1C
mce1C
Bin Zhao, Oliver He
mceD
WEB: http://www.ncbi.nlm.nih.gov/gene
886810
Rv0170
20140215
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
209
Mce-family protein Mce1B
-
mce1B
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886812
Rv0168
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: yrbE1B mutant is attenuated in mice [PMID:15804490].
210
Conserved integral membrane protein YrbE1B
yrbE1B
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886822
Rv0166
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20214478; 20980199
MUTATION: fadD5 mutant is attenuated in mice [PMID:20214478].
211
Probable fatty-acid-CoA ligase FadD5 (fatty-acid-CoA synthetase) (fatty-acid-CoA synthase)
fadD5
Bin Zhao, Oliver He
mce1
WEB: http://www.ncbi.nlm.nih.gov/gene
886823
Rv0169
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 15804490; 16620748; 17046327; 20980199
MUTATION: attenuated in mice [PMID:14569030].
212
Mce-family protein Mce1A
-
mce1A
Bin Zhao, Oliver He
fadD33
WEB: http://www.ncbi.nlm.nih.gov/gene
886855
Rv1345
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: fadD33 mutant is attenuated in mice [PMID:12480891].
213
Probable fatty acyl-AMP ligase MbtM
-
mbtM
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886866
Rv1338
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 18757813; 20980199
MUTATION: attenuated in mice [PMID:14569030].
214
Probable glutamate racemase MurI
murI
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886882
Rv1333
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
215
Probable hydrolase
Rv1333
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886901
Rv1332
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
216
Probable transcriptional regulatory protein
Rv1332
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886904
Rv1323
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
217
Probable acetyl-CoA acetyltransferase FadA4 (acetoacetyl-CoA thiolase)
fadA4
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886931
Rv0100
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
218
hypothetical protein
Rv0100
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886933
Rv0099
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199; 23625916
MUTATION: attenuated in mice [PMID:14569030].
219
Possible fatty-acid-CoA ligase FadD10 (fatty-acid-CoA synthetase) (fatty-acid-CoA synthase)
fadD10
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886935
Rv0098
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199; 22292955
MUTATION: attenuated in mice [PMID:14569030].
220
Probable fatty acyl CoA thioesterase type III FcoT
fcoT
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886941
Rv1304
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
221
Probable ATP synthase a chain AtpB (protein 6)
atpB
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886951
Rv0101
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION attenuated in mice [PMID:14569030].
222
Probable peptide synthetase Nrp (peptide synthase)
nrp
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886960
Rv1293
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 16511157; 19543810; 20980199
MUTATION: lysA mutant is markedly attenuated in SCID mice, and is strongly attenuated in mice when in combination with a secA2 mutation [PMID:21264335].
4915
Diaminopimelate decarboxylase LysA (DAP decarboxylase)
lysA
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
886987
Rv1284
20131130
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 15753099; 20980199
MUTATION: attenuated in mice [PMID:14569030].
223
Beta-carbonic anhydrase
canA
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887021
Rv1272c
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
224
Probable drugs-transport transmembrane ATP-binding protein ABC transporter
Rv1272c
Bin Zhao, Oliver He
tbINO
WEB: http://www.ncbi.nlm.nih.gov/gene
887028
Rv0046c
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: ino1 mutant is attenuated in resting macrophages and guinea pigs [PMID:14763976].
225
myo-inositol-1-phosphate synthase Ino1 (inositol 1-phosphate synthetase) (D-glucose 6-phosphate cycloaldolase) (glucose 6-phosphate cyclase) (glucocycloaldolase)
-
ino1
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887093
Rv1244
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
226
Probable lipoprotein LpqZ
lpqZ
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887104
Rv1238
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199; 21118978
MUTATION: attenuated in mice [PMID:14569030]
227
Probable sugar-transport ATP-binding protein ABC transporter SugC
sugC
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887121
Rv1237
20131130
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199; 21118978
MUTATION: attenuated in mice [PMID:14569030].
228
Probable sugar-transport integral membrane protein ABC transporter SugB
sugB
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887124
Rv1236
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199; 21118978
MUTATION: attenuated in mice [PMID:14569030].
229
Probable sugar-transport integral membrane protein ABC transporter SugA
sugA
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887143
Rv1224
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
230
Probable protein TatB
tatB
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887145
Rv1235
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199; 21118978
MUTATION: attenuated in mice [PMID:14569030].
231
Probable sugar-binding lipoprotein LpqY
lpqY
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887168
Rv2502c
20140329
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
232
Probable acetyl-/propionyl-CoA carboxylase (beta subunit) AccD1
accD1
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887170
Rv0485
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 19651861; 20980199
MUTATION: Rv0485 mutant is attenuated in mice [PMID:19651861].
233
Possible transcriptional regulatory protein
Rv0485
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887173
Rv2885c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
234
Probable transposase
Rv2885c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887185
Rv0490
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: senX3-regX3 deletion mutant is attenuated in mice [PMID:12777483].
235
Putative two component sensor histidine kinase SenX3
senX3
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887195
Rv0491
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 17942407; 20980199
MUTATION: senX3-regX3 deletion mutant is attenuated in mice [PMID:12777483].
236
Two component sensory transduction protein RegX3 (transcriptional regulatory protein) (probably LuxR-family)
regX3
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887204
Rv3574
20140217
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
237
Transcriptional regulatory protein KstR (probably TetR-family)
kstR
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887205
Rv2921c
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
238
Probable cell division protein FtsY (SRP receptor) (signal recognition particle receptor)
ftsY
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887233
Rv2211c
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
239
Probable aminomethyltransferase GcvT (glycine cleavage system T protein)
gcvT
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887235
Rv3551
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
240
Possible CoA-transferase (alpha subunit)
Rv3551
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887246
Rv2241
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 16045627; 20980199
MUTATION: attenuated in mice [PMID:14569030].
241
Pyruvate dehydrogenase E1 component AceE (pyruvate decarboxylase) (pyruvate dehydrogenase) (pyruvic dehydrogenase)
aceE
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887247
Rv3519
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
242
hypothetical protein
Rv3519
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887255
Rv2472
20131130
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
243
hypothetical protein
Rv2472
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887256
Rv0500
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: proC mutant is attenuated in mice [PMID:11160012].
244
Probable pyrroline-5-carboxylate reductase ProC (P5CR) (P5C reductase)
proC
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887285
Rv3556c
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
245
Probable acetyl-CoA acetyltransferase FadA6 (acetoacetyl-CoA thiolase)
fadA6
Bin Zhao, Oliver He
ilvB
WEB: http://www.ncbi.nlm.nih.gov/gene
887286
Rv3003c
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 19542000; 20884690; 20980199
MUTATION: ilvB1 mutant is attenuated in mice [PMID:19542000].
246
Acetolactate synthase (large subunit) IlvB1 (acetohydroxy-acid synthase)
-
ilvB1
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887291
Rv2947c
20140217
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: pks15 mutant is attenuated in mice [PMID:12730158].
247
Probable polyketide synthase Pks15
pks15
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887313
Rv2702
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
248
Polyphosphate glucokinase PpgK (polyphosphate-glucose phosphotransferase)
ppgK
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887410
Rv2976c
20131207
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 17142904; 20693660; 20980199
MUTATION: attenuated in mice [PMID:14569030].
249
Probable uracil-DNA glycosylase Ung (UDG)
ung
Bin Zhao, Oliver He
acoas
WEB: http://www.ncbi.nlm.nih.gov/gene
887454
Rv2941
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: fadD28 mutant is attenuated in mice [PMID:10573420].
250
Fatty-acid-AMP ligase FadD28 (fatty-acid-AMP synthetase) (fatty-acid-AMP synthase)
-
fadD28
Bin Zhao, Oliver He
trkA
trkB
WEB: http://www.ncbi.nlm.nih.gov/gene
887493
Rv2692
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
251
TRK system potassium uptake protein CeoC
-
ceoC
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887548
Rv2942
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 16879801; 20980199
MUTATION: mmpL7 mutant is attenuated in mice [PMID:10573420].
252
Conserved transmembrane transport protein MmpL7
mmpL7
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887552
Rv1204c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
253
hypothetical protein
Rv1204c
Bin Zhao, Oliver He
acr
WEB: http://www.ncbi.nlm.nih.gov/gene
887579
Rv2031c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 15545279; 15860225; 16428728; 16784488; 16930542; 17194806; 19874551; 20980199; 22504645; 22984534; 23133523
MUTATION: hspX mutant is attenuated in murine macrophages and THP-1 cells [PMID:9689123].
254
Heat shock protein HspX (alpha-crystallin homolog) (14 kDa antigen) (HSP16.3)
-
hspX
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887594
Rv3414c
20140215
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199; 23314154
MUTATION: sigD mutant is attenuated in human macrophages and mice [PMID:15659067].
255
Probable alternative RNA polymerase sigma-D factor SigD
sigD
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887595
Rv3419c
20131130
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
256
Probable O-sialoglycoprotein endopeptidase Gcp (glycoprotease)
gcp
Bin Zhao, Oliver He
whmB
WEB: http://www.ncbi.nlm.nih.gov/gene
887598
Rv3416
20140215
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 16923787; 17609386; 20980199
MUTATION: whiB3 mutant is attenuated in mice [PMID:11880648].
257
Transcriptional regulatory protein WhiB-like WhiB3 Contains [4FE-4S] cluster
-
whiB3
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887603
Rv2930
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 15749014; 20553505; 20980199
MUTATION: fadD26 mutant is attenuated in mice [PMID:15958066].
258
Fatty-acid-AMP ligase FadD26 (fatty-acid-AMP synthetase) (fatty-acid-AMP synthase)
fadD26
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887617
Rv3061c
20140217
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
259
Probable acyl-CoA dehydrogenase FadE22
fadE22
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887633
Rv0566c
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
260
hypothetical protein
Rv0566c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887681
Rv2192c
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 16337227; 20980199; 23363292
MUTATION: trpD mutant is attenuated in mice [PMID:11160012].
261
Probable anthranilate phosphoribosyltransferase TrpD
trpD
Bin Zhao, Oliver He
hsd4A
WEB: http://www.ncbi.nlm.nih.gov/gene
887697
Rv3502c
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
262
Probable short-chain type dehydrogenase/reductase Possible 17-beta-hydroxysteroid dehydrogenase
-
Rv3502c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887744
Rv2483c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199; 24359335
MUTATION: attenuated in mice [PMID:14569030].
263
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)
plsC
Bin Zhao, Oliver He
mce2
WEB: http://www.ncbi.nlm.nih.gov/gene
887745
Rv0589
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 15804490; 20980199
MUTATION: mce2A mutant is attenuated in mice [PMID:15804490].
264
Mce-family protein Mce2A
-
mce2A
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887750
Rv2707
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 18096644; 20980199
MUTATION: attenuated in mice [PMID:14569030].
265
Probable conserved transmembrane alanine and leucine rich protein
Rv2707
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887782
Rv3545c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 19146393; 19846551; 19846552; 20545858; 20980199
MUTATION: attenuated in mice [PMID:14569030].
266
Probable cytochrome P450 125 Cyp125
cyp125
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887815
Rv3042c
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
267
Probable phosphoserine phosphatase SerB2 (PSP) (O-phosphoserine phosphohydrolase) (pspase)
serB2
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887818
Rv3563
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
268
Probable acyl-CoA dehydrogenase FadE32
fadE32
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887836
Rv3588c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 15753099; 16321983; 20980199
MUTATION: attenuated in mice [PMID:14569030].
269
Beta-carbonic anhydrase CanB
canB
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887838
Rv3560c
20140329
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
270
Probable acyl-CoA dehydrogenase FadE30
fadE30
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887857
Rv2224c
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
271
Probable carboxylesterase CaeA
caeA
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887888
Rv2583c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 16026164; 20980199
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].
272
Probable GTP pyrophosphokinase RelA (ATP:GTP 3'-pyrophosphotransferase) (PPGPP synthetase I) ((P)PPGPP synthetase) (GTP diphosphokinase)
relA
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887893
Rv2040c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
273
Probable sugar-transport integral membrane protein ABC transporter
Rv2040c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887917
Rv2693c
20131207
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: Rv2693c mutant is attenuated in mice [PMID:17353284].
274
Probable conserved integral membrane alanine and leucine rich protein
Rv2693c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887918
Rv3400
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
275
Probable hydrolase
Rv3400
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887956
Rv2945c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
276
Probable conserved lipoprotein LppX
lppX
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887968
Rv2937
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
277
Daunorubicin-dim-transport integral membrane protein ABC transporter DrrB
drrB
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887990
Rv1211
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
278
hypothetical protein
Rv1211
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
887998
Rv2038c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
279
Probable sugar-transport ATP-binding protein ABC transporter
Rv2038c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888006
Rv3472
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
280
hypothetical protein
Rv3472
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888017
Rv2912c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
281
Probable transcriptional regulatory protein (probably TetR-family)
Rv2912c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888029
Rv3335c
20131207
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
282
Probable conserved integral membrane protein
Rv3335c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888031
Rv0636
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 17906131; 18048930; 20980199
MUTATION: attenuated in mice [PMID:14569030].
283
(3R)-hydroxyacyl-ACP dehydratase subunit HadB
hadB
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888053
Rv3371
20131130
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
284
Possible triacylglycerol synthase (diacylglycerol acyltransferase)
Rv3371
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888058
Rv0643c
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
285
Methoxy mycolic acid synthase 3 MmaA3 (methyl mycolic acid synthase 3) (MMA3) (hydroxy mycolic acid synthase)
mmaA3
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888064
Rv3375
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
286
Probable amidase AmiD (acylamidase) (acylase)
amiD
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888073
Rv3377c
20140215
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 15719101; 19574210; 20980199
MUTATION: Rv3377c mutant is attenuated in survival inside of macrophages [PMID:15340136].
287
Halimadienyl diphosphate synthase
Rv3377c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888075
Rv3378c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199; 21228491
MUTATION: Rv3378c mutant is attenuated in survival within macrophages [PMID:15340136].
288
Diterpene synthase
Rv3378c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888081
Rv0655
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
289
Possible ribonucleotide-transport ATP-binding protein ABC transporter Mkl
mkl
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888091
Rv3544c
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 18486437; 20980199
MUTATION: attenuated in mice [PMID:14569030].
290
Probable acyl-CoA dehydrogenase FadE28
fadE28
Bin Zhao, Oliver He
rpoE
WEB: http://www.ncbi.nlm.nih.gov/gene
888094
Rv3223c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 18192397; 19376862; 20980199
MUTATION: sigH mutant has diminished immunopathology and is nonlethal in mice [PMID:12060776].
291
Alternative RNA polymerase sigma-E factor (sigma-24) SigH (RPOE)
-
sigH
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888107
Rv2206
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: Rv2206 mutant is attenuated in mice [PMID:17353284].
292
Probable conserved transmembrane protein
Rv2206
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888122
Rv2946c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 15308633; 20980199
MUTATION: pks1 mutant is attenuated in mice [PMID:12730158].
293
Probable polyketide synthase Pks1
pks1
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888168
Rv2936
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
294
Daunorubicin-dim-transport ATP-binding protein ABC transporter DrrA
drrA
Bin Zhao, Oliver He
nfo
WEB: http://www.ncbi.nlm.nih.gov/gene
888190
Rv0670
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
295
Probable endonuclease IV End (endodeoxyribonuclease IV) (apurinase)
-
end
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888225
Rv2987c
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 19194004; 20980199
MUTATION: leuD mutant is attenuated in mice [PMID:10768986].
296
Probable 3-isopropylmalate dehydratase (small subunit) LeuD (isopropylmalate isomerase) (alpha-IPM isomerase) (IPMI)
leuD
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888228
Rv2553c
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
297
Probable conserved membrane protein
Rv2553c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888247
Rv3523
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
298
Probable lipid carrier protein or keto acyl-CoA thiolase Ltp3
ltp3
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888279
Rv0687
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
299
Probable short-chain type dehydrogenase/reductase
Rv0687
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888295
Rv3527
20131130
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: Rv3527 mutant is attenuated for intramacrophage survival [PMID:15340136].
300
Hypothetical protein
Rv3527
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888303
Rv2734
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
301
hypothetical protein
Rv2734
Bin Zhao, Oliver He
supA
WEB: http://www.ncbi.nlm.nih.gov/gene
888320
Rv3501c
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
302
Conserved integral membrane protein YrbE4A Possible ABC transporter
-
yrbE4A
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888321
Rv2072c
20140329
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
303
Precorrin-6Y C(5,15)-methyltransferase (decarboxylating) CobL
cobL
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888337
Rv2231c
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
304
Possible aminotransferase CobC
cobC
Bin Zhao, Oliver He
mce4
WEB: http://www.ncbi.nlm.nih.gov/gene
888344
Rv3499c
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 18201981; 19019220; 20980199; 23622789
MUTATION: attenuated in mice [PMID:14569030].
305
Mce-family protein Mce4A
-
mce4A
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888350
Rv2048c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 15611286; 20980199
MUTATION: pks12 mutant is attenuated in mice [PMID:12819062].
306
Polyketide synthase Pks12
pks12
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888354
Rv3497c
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
307
Mce-family protein Mce4C
mce4C
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888355
Rv2275
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
308
hypothetical protein
Rv2275
Bin Zhao, Oliver He
mce4E
WEB: http://www.ncbi.nlm.nih.gov/gene
888364
Rv3495c
20131130
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
309
Possible Mce-family lipoprotein LprN (Mce-family lipoprotein Mce4E)
-
lprN
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888387
Rv3534c
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
310
Probable 4-hydroxy-2-oxovalerate aldolase (HOA)
hsaF
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888410
Rv3489
20131207
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
311
hypothetical protein
Rv3489
Bin Zhao, Oliver He
ddl
WEB: http://www.ncbi.nlm.nih.gov/gene
888415
Rv2981c
20140405
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199; 23286234
MUTATION: attenuated in mice [PMID:14569030].
312
Probable D-alanine--D-alanine ligase DdlA (D-alanylalanine synthetase) (D-ala-D-ala ligase)
-
ddlA
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888430
Rv3487c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 15939293; 17434691; 17869077; 18535356; 18649013; 20980199
MUTATION: lipF mutant is attenuated in mice lungs [PMID:10564470].
313
Probable esterase/lipase LipF
lipF
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888445
Rv3484
20140215
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
314
Possible conserved protein CpsA
cpsA
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888450
Rv3540c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
315
Probable lipid transfer protein or keto acyl-CoA thiolase Ltp2
ltp2
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888475
Rv3541c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
316
hypothetical protein
Rv3541c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888482
Rv2696c
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
317
Conserved alanine and glycine and valine rich protein
Rv2696c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888486
Rv3542c
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
318
hypothetical protein
Rv3542c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888491
Rv2938
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: drrC mutant is attenuated in mice [PMID:10564470].
319
Probable daunorubicin-dim-transport integral membrane protein ABC transporter DrrC
drrC
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888498
Rv2277c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
320
Possible glycerolphosphodiesterase
Rv2277c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888539
Rv2845c
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
321
Probable prolyl-tRNA synthetase ProS (proline--tRNA ligase) (PRORS) (global RNA synthesis factor) (proline translase)
proS
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888560
Rv2857c
20131207
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
322
Probable short-chain type dehydrogenase/reductase
Rv2857c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888570
Rv2813
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
323
hypothetical protein
Rv2813
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888609
Rv0735
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 16199577; 20980199
MUTATION: sigL mutant is attenuated in mice [PMID:16199577].
324
Probable alternative RNA polymerase sigma factor SigL
sigL
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888646
Rv2998
20131130
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
325
Hypothetical protein
Rv2998
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888653
Rv3087
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
326
Possible triacylglycerol synthase (diacylglycerol acyltransferase)
Rv3087
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888694
Rv3258c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
327
hypothetical protein
Rv3258c
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888705
Rv3270
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199; 21925112; 23482562
MUTATION: attenuated in mice [PMID:14569030].
328
Probable metal cation-transporting P-type ATPase C CtpC
ctpC
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888723
Rv2069
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 16735723; 20980199; 22015173
MUTATION: sigC mutant is attenuated in mice [PMID:15049808].
329
RNA polymerase sigma factor, ECF subfamily, SigC
sigC
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888727
Rv3286c
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 16735723; 20980199
MUTATION: sigF mutant is attenuated in mice [PMID:14977982].
330
Alternative RNA polymerase sigma factor SigF
sigF
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888729
Rv3277
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
331
Probable conserved transmembrane protein
Rv3277
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888743
Rv3246c
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 16629667; 17511470; 20223818; 20843371; 20980199; 22610443
MUTATION: attenuated in mice [PMID:14569030].
332
Two component sensory transduction transcriptional regulatory protein MtrA
mtrA
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888751
Rv1221
20140406
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 16513743; 18192397; 18606740; 18657035; 20980199
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].
333
Alternative RNA polymerase sigma factor SigE
sigE
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888772
Rv0757
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 16573683; 18052041; 18065542; 18065544; 18282096; 18757548; 18946503; 19820095; 20363229; 20814030; 20980199; 21634789; 22072719; 22880126
MUTATION: phoP mutant is attenuated in mice [PMID:11454210].
334
Possible two component system response transcriptional positive regulator PhoP
phoP
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888778
Rv3168
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199; 21543877
MUTATION: attenuated in mice [PMID:14569030].
335
Putative aminoglycoside phosphotransferase
Rv3168
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888779
Rv3114
20140222
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
336
hypothetical protein
Rv3114
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888786
Rv3178
20140215
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
337
hypothetical protein
Rv3178
Bin Zhao, Oliver He
WEB: http://www.ncbi.nlm.nih.gov/gene
888798
Rv3103c
20140322
83332
protein-coding
NCBI-supplied
PMID: 9634230; 12368430; 20980199
MUTATION: attenuated in mice [PMID:14569030].
338