biocarta(graphite)
biocarta()所属R语言包：graphite
BioCarta pathways
BioCarta通路
译者：生物统计家园网 机器人LoveR
描述----------Description----------
A list with a pathway object for each BioCarta pathway.
的对象每个BioCarta途径pathway名单。
http://www.biocarta.com
通路的拓扑结构转换----------Pathway topology conversion----------
BioCarta pathways were retrieved in BioPax format from the PDI database web page.
在从交车数据库网页BioPax格式检索BioCarta通路。
We define a pathway for each BioPax tag “pathway”. Pathway nodes often correspond to multiple gene products. These can be divided into protein complexes (proteins linked by protein-protein interactions) and groups made of alternative members (genes with similar biochemical functions). Thus, when considering signal propagation these groups are considered differently. The first kind (hereafter group AND) should be expanded into a clique (all proteins connected to the others), while the second (hereafter group OR) should be expanded without connection among them. In the BioPax format only one type of group is allowed: protein complexes (group AND) with the tag 'complex'. However, it often happens that the 'protein' tag contains multiple 'xref' pointing to alternative elements of the process (group OR).
我们定义每个BioPax标签“通路”的一个途径。通路节点往往对应多个基因产物。这些可分为蛋白复合物（蛋白质蛋白质相互作用链接）和替代成员（具有类似的生化功能的基因）的群体。因此，当考虑信号传播这些群体被认为是不同的。第一类（以下简称组）应扩大成集团（连接到其他所有的蛋白质），而第二个（以下简称集团或）应扩大没有它们之间的连接。只有一组类型在BioPax格式允许：“复杂的”标签的蛋白复合物（组）。但是，它经常发生，“蛋白”标签包含多个“外部参照”，指向过程中的替代元素（组）。
Compound mediated interactions are interactions for which a compound acts as a bridge between two elements. Since chemical compounds are not usually measured with high-throughput technology, they should be removed from the network to analyse gene signals. However, the trivial elimination of the compounds, without signal propagation, will strongly bias the topology interrupting the signals that pass through them. If element 'A' is linked to compound 'c' and compound 'c' is linked to element 'B', element 'A' should be linked to element 'B'. Not all compounds are considered for the propagation because some of them (for example: H2O, ATP, ADP) are highly frequent in map descriptions and the signal propagation through them would lead to chains too long. Compounds not considered for propagation are not characteristic of a specific reaction, but act as secondary substrates/products widely shared among different processes.
复合介导的相互作用是相互作用的化合物，其中两个元素之间的桥梁作用。由于化合物通常不高通量技术来衡量，他们应该被从网络分析基因信号。然而，化合物的琐碎消除无信号传播，会强烈偏见的拓扑中断，通过他们传递的信号。如果元素一挂c和C是复合元素“B”复合元素“A”应与元素“B”。并非所有的化合物被认为是为传播，因为他们中的一些（例如：水，三磷酸腺苷，ADP）中是非常频繁的，在图上描述，并通过它们的信号传播，会导致链太长。不考虑繁殖的化合物不是一个特定的反应的特点，但作为辅助基板/产品广泛应用于不同的进程之间共享。
graphite allows the user to see the single/multiple relation types that characterized an edge. The type of edges have been kept as much as possible similar to those annotated in the original data format. Some new types have been introduced due to topological conversion needs.
石墨允许用户看到单一/多重关系类型特征的边缘。边一直维持在尽可能多的原始数据格式类似这些注释。由于拓扑转换的需要，相继出台了一些新的类型。
参见----------See Also----------
pathway-class.
pathway-class。
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
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发表于 2012-2-25 21:02:33
