KEGG Pathway数据结构

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所属分类:生物信息学

实体关系图

KEGG Pathway数据结构

实体

名称定义Pathwayspecifies graph information stored in the KEGG pathway map代谢通路图path:ko00010EntryThe entry element contains information about a node of the pathway.节点信息Componenta subelement of the entry element, and is used when the entry element is a complex node; namely, when the type attribute value of the entry element is “group”.组件,一个复杂的节点,比如节点为Group类型时,包含的节点,可以存放到组件中Graphicsa subelement of the entry element, specifying drawing information about the graphics object.节点在图位信息Relationrelationship between two proteins (gene products) or two KOs (ortholog groups) or protein and compound, which is indicated by an arrow or a line connecting two nodes in the KEGG pathways.节点之间的关系Subtypemore detailed information about the nature of the interaction or the relation.节点之间关系的更详细信息Reactionchemical reaction between a substrate and a product indicated by an arrow connecting two circles in the KEGG pathways.在KEGG通路中,用两个圆圈加箭头表示底物与产物之间的化学反应。rn:(accession)rn:R02749Substratethe substrate node of this reaction.反应的底物cpd:(accession)

gl:(accession)Productthe product node of this reaction.产物cpd:(accession)

gl:(accession)Altthe alternative name of its parent element.别名cpd:(accession)

gl:(accession)

节点的类型

attribute valueexplanationpath:(accession)pathway map

ex) name=”path:map00040″ko:(accession)KO (ortholog group)

ex) name=”ko:E3.1.4.11″ec:(accession)enzyme 酶

ex) name=”ec:1.1.3.5″rn:(accession)reaction 反应

ex) name=”rn:R00120″cpd:(accession)chemical compound 化合物

ex) name=”cpd:C01243″gl:(accession)glycan 多糖

ex) name=”gl:G00166″[org prefix]:(accession)gene product of a given organism 基因产物

ex) name=”eco:b1207″group:(accession)complex of KOs 组

If accession is undefined, “undefined” is specified.

ex) name=”group:ORC”

节点关联的类型

attribute value

explanation

ECrel

enzyme-enzyme relation, indicating two enzymes catalyzing successive reaction steps

酶与酶的关系,表明这两种酶催化逐次反应步骤

PPrel

protein-protein interaction, such as binding and modification

蛋白质与蛋白质相互作用,比如绑定与修饰

GErel

gene expression interaction, indicating relation of transcription factor and target gene product

基因表达的相互作用,表明转录因子与靶基因产物的关系

PCrel

protein-compound interaction

蛋白质与化合物相互作用

maplink

link to another map

链接到另一个图谱

关联或者相互作用的进一步明细

name

value

ECrel

PPrel

GErel

Explanation

compound

Entry element id attribute value for compound.

*

*

shared with two successive reactions (ECrel) or intermediate of two interacting proteins (PPrel)

两个连续反应的共享复合物

另个相互作用蛋白质的中间体

hidden compound

Entry element id attribute value for hidden compound.

*

shared with two successive reactions but not displayed in the pathway map

隐含的复合物

activation

–>

*

positive and negative effects which may be associated with molecular information below

激活

inhibition

–|

*

抑制

expression

–>

*

interactions via DNA binding

表达

repression

–|

*

抑制

indirect effect

..>

*

*

indirect effect without molecular details

间接影响

state change

*

state transition

状态改变

binding/association

*

association and dissociation

绑定或者结合

dissociation

-+-

*

解离

missing interaction

-/-

*

*

missing interaction due to mutation, etc.

由于突变,缺失的相互作用

phosphorylation

+p

*

molecular events 分子水平

磷酸化

dephosphorylation

-p

*

去磷酸化

glycosylation

+g

*

糖基化

ubiquitination

+u

*

泛素化

methylation

+m

*

甲基化

数据的获取

所有的pathway信息,可以下载XML文件,解析XML文件可以得到该pathway的所有数据,如果只是需要部分数据,可以在程序中直接调用KEGG提供的API。

相关链接

http://www.kegg.jp/kegg/xml/docs/http://www.kegg.jp/kegg/soap/doc/keggapi_manual.html原文链接:KEGG Pathway数据结构 http://boyun.sh.cn/bio/?p=1857

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