R语言 ontoCAT包 Ontology-class()函数中文帮助文档(中英文对照)

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Ontology-class(ontoCAT)
Ontology-class()所属R语言包：ontoCAT

                                        Class "Ontology"
                                         类“本体论”

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Supports basic operations with ontologies: traversal and search
支持本体的基本操作：遍历和搜索


访问本体----------Accessing the ontologies----------

The appropriate way to access ontology is via the helper getOntology function.
助手getOntology函数是通过适当的方式来访问本体。


访问的自由振荡----------Accessing the EFO----------

The appropriate way to access EFO is via the helper getEFO function.
助手getEFO函数是通过适当的方式来存取自由振荡。


插槽----------Slots----------




ontology: Object of class "jobjRef" No user-serviceable parts inside. Maps to an internal Java Ontology object.
ontology类"jobjRef"无用户可维修的部件对象。内部的Java本体对象的图。


方法----------Methods----------




getAllTermChildren signature(object1 = "Ontology", object2 = "OntologyTerm"): Returns list of term's all children
getAllTermChildrensignature(object1 = "Ontology", object2 = "OntologyTerm")：返回术语列表是所有儿童




getAllTermChildrenById signature(object = "Ontology", id = "character"): Returns list of term's all children
getAllTermChildrenByIdsignature(object = "Ontology", id = "character")：返回术语列表是所有的孩子




getAllTermIds signature(object = "Ontology"): Returns list of all term accessions
getAllTermIdssignature(object = "Ontology")：返回所有术语加入列表




getAllTermParents signature(object1 = "Ontology", object2 = "OntologyTerm"): Returns list of term's all parents
getAllTermParentssignature(object1 = "Ontology", object2 = "OntologyTerm")：返回列表学期的所有家长




getAllTermParentsById signature(object = "Ontology", id = "character"): Returns list of term's all parents
getAllTermParentsByIdsignature(object = "Ontology", id = "character")：返回列表学期的所有家长




getAllTerms signature(object = "Ontology"): Returns list of all terms
getAllTermssignature(object = "Ontology")：返回列表中的所有条款




getEFOBranchRootIds signature(object = "Ontology"): Returns set of branch root accessions. Method specific for EFO ontology
getEFOBranchRootIdssignature(object = "Ontology")：返回分支的根加入。自由振荡本体方法的具体




getOntologyAccession signature(object = "Ontology"): Returns parsed ontology accession
getOntologyAccessionsignature(object = "Ontology")：返回解析本体加入




getOntologyDescription signature(object = "Ontology"): Returns parsed ontology description
getOntologyDescription的signature(object = "Ontology")：返回解析的本体描述




getRootIds signature(object = "Ontology"): Returns list of root terms accessions, if there are any
getRootIdssignature(object = "Ontology")：返回根条款加入列表，如果有任何




getRoots signature(object = "Ontology"): Returns list of root terms, if there are any
getRootssignature(object = "Ontology")：返回根条款列表，如果有任何




getTermAndAllChildren signature(object1 = "Ontology", object2 = "OntologyTerm"): Returns list of accessions of term itself and all its children recursively
getTermAndAllChildrensignature(object1 = "Ontology", object2 = "OntologyTerm")：返回一词本身和其所有的孩子递归加入列表




getTermAndAllChildrenById signature(object = "Ontology", id = "character"): Returns list of accessions of term itself and all its children recursively
getTermAndAllChildrenByIdsignature(object = "Ontology", id = "character")：返回词本身和所有的孩子递归加入列表




getTermById signature(object = "Ontology", id = "character"):  Fetch term by accession. Returns external term representation if found in ontology, null otherwise
通过加入getTermByIdsignature(object = "Ontology", id = "character")：获取术语。如果发现在本体返回外部术语代表性，否则返回null




getTermChildren signature(object1 = "Ontology", object2 = "OntologyTerm"): Returns list of term's direct children
getTermChildren术语的直接孩子signature(object1 = "Ontology", object2 = "OntologyTerm")：返回列表




getTermChildrenById signature(object = "Ontology", id = "character"): Returns list of term's direct children
getTermChildrenById术语的直接孩子signature(object = "Ontology", id = "character")：返回列表




getTermDefinitions signature(object1 = "Ontology", object2 = "OntologyTerm"): Returns set of term's definitions if there are some
getTermDefinitionssignature(object1 = "Ontology", object2 = "OntologyTerm")：集返回一词的定义是否有一些




getTermNameById signature(object = "Ontology", id = "character"): Returns term's label by accession
getTermNameByIdsignature(object = "Ontology", id = "character")：返回加入术语的标签




getTermParents signature(object1 = "Ontology", object2 = "OntologyTerm"):  Returns list of term's direct parents
getTermParents术语的直接家长signature(object1 = "Ontology", object2 = "OntologyTerm")：返回列表




getTermParentsById signature(object = "Ontology", id = "character"):  Returns list of term's direct parents
getTermParentsById术语的直接家长signature(object = "Ontology", id = "character")：返回列表




getTermSynonyms signature(object1 = "Ontology", object2 = "OntologyTerm"): Returns set of term's synonyms  if there are some
getTermSynonymssignature(object1 = "Ontology", object2 = "OntologyTerm")：返回术语的同义词，如果有一些




hasTerm signature(object = "Ontology", id = "character"): Check if term with specified accession exists in ontology
hasTermsignature(object = "Ontology", id = "character")：是否术语指定加入本体存在




isEFOBranchRoot signature(object1 = "Ontology", object2 = "OntologyTerm"): Returns true if term is branch root of EFO. Method specific for EFO ontology
isEFOBranchRootsignature(object1 = "Ontology", object2 = "OntologyTerm")：返回true，如果术语是分支根的谱线。自由振荡本体方法的具体




isEFOBranchRootById signature(object = "Ontology", id = "character"): Returns true if term is branch root of EFO. Method specific for EFO ontology
isEFOBranchRootByIdsignature(object = "Ontology", id = "character")：返回true，如果术语是分支根的谱线。自由振荡本体方法的具体




isRoot signature(object1 = "Ontology", object2 = "OntologyTerm"): Returns true if term is root of ontology
isRootsignature(object1 = "Ontology", object2 = "OntologyTerm")：返回true，如果术语是本体的根




isRootById signature(object = "Ontology", id = "character"): Returns true if term is root of ontology
isRootByIdsignature(object = "Ontology", id = "character")：返回true，如果术语是本体的根




searchTerm signature(object = "Ontology", id = "character"): Searches for term in ontology by name
searchTerm的signature(object = "Ontology", id = "character")：搜索本体术语的名字




searchTermPrefix signature(object = "Ontology", prefix = "character"): Searches for prefix in ontology
searchTermPrefixsignature(object = "Ontology", prefix = "character")：搜索本体的前缀




showHierarchyDownToTerm signature(object1 = "Ontology", object2 = "OntologyTerm"): Returns set of terms that represent ontology "opened" down to specified term, hence displaying all its parents first and then a tree level, containing specified term
showHierarchyDownToTermsignature(object1 = "Ontology", object2 = "OntologyTerm")：返回的条款，代表本体设定“开”到指定的期限，因此首先显示其所有的父母，然后一棵树的水平，包含指定的期限




showHierarchyDownToTermById signature(object = "Ontology", id = "character"): Returns set of terms that represent ontology "opened" down to specified term, hence displaying all its parents first and then a tree level, containing specified term
showHierarchyDownToTermByIdsignature(object = "Ontology", id = "character")：返回表示本体的条款设置“打开”下调至指定的期限，因此，首先显示其所有的父母，然后一棵树的水平，包含指定的期限




showPathsToTerm signature(object1 = "Ontology", object2 = "OntologyTerm"): Returns paths to the specified term from ontology's root term
showPathsToTermsignature(object1 = "Ontology", object2 = "OntologyTerm")：返回路径到指定的期限，从本体论的根术语




showPathsToTermById signature(object = "Ontology", id = "character"): Returns paths to the specified term from ontology's root term
showPathsToTermByIdsignature(object = "Ontology", id = "character")：返回路径到指定的期限，从本体论的根术语




getOntologyRelationNames signature(object = "Ontology"): Returns list of relations used in ontology
getOntologyRelationNamessignature(object = "Ontology")：返回列表的关系，在本体论




getTermRelationNames signature(object1 = "Ontology", object2 = "OntologyTerm"): Returns list of relations that term has
getTermRelationNamessignature(object1 = "Ontology", object2 = "OntologyTerm")：返回列表的关系，术语有




getTermRelationNamesById signature(object1 = "Ontology", id = "character"): Returns list of relations that term under given accession has
getTermRelationNamesByIdsignature(object1 = "Ontology", id = "character")：返回列表下加入的术语有关系




getTermRelations signature(object1 = "Ontology", object2 = "OntologyTerm", relation = "character"): Returns list of terms that are in defined relation with term of interest
getTermRelationssignature(object1 = "Ontology", object2 = "OntologyTerm", relation = "character")：返回列表中定义的长远利益的关系的条款




getTermRelations signature(object = "Ontology", id = "character", relation = "character"): Returns list of terms that are in defined relation with term of interest
getTermRelationssignature(object = "Ontology", id = "character", relation = "character")：返回列表中定义的长远利益的关系的条款


注意----------Note----------

This package ships with the EFO OWL file, version released at the time of the package build. Provided EFO OWL file can be loaded as any other OWL or OBO file by using getOntology function.
这个包船舶的自由振荡OWL文件，版本发布在包建立的时间。提供自由振荡OWL文件可以加载任何其他的OWL或OBO的文件使用getOntology功能。

Another option is to load the latest EFO version on the fly by using getEFO function.
另一种选择是装载在飞行中使用getEFO功能的最新版本的自由振荡。


作者（S）----------Author(s)----------


Natalja Kurbatova



参考文献----------References----------







参见----------See Also----------

getOntology,getEFO and OntologyTerm
getOntology，getEFO和OntologyTerm


举例----------Examples----------


    ontology <- getEFO()
    getEFOBranchRootIds(ontology)
    term <- getTermById(ontology,"EFO_0001221")
    getTermParents(ontology,term)
    searchTermPrefix(ontology,"leuk")
    getTermAndAllChildrenById(ontology,"EFO_0000318")
    searchTerm(ontology,"thymus")
    ontology <- getOntology("http://www.ebi.ac.uk/efo/efo.owl")
    ontology <- getOntology("./ontoCAT/extdata/cell.obo")
    getAllTermIds(ontology)
   

转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。


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