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 &gt; 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 &gt; 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 &gt; 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 &gt; 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 &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; 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 &gt;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&lt;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 &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; 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