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Controlled vocabularies and semantics in systems biology (Introduction (1…
Controlled vocabularies and semantics in systems biology
Introduction
1.The form models take in systems biology change a lot during these years. Traditional不好，Formal quantitative models replace the tradition and enable meaningful comparison between assumption and empirical facts.
2.Biology中的Model很多，增长很快，需要standardization，介绍了三个standardization: content(what information)，syntax(xml), semantic(unified common definition for all words phrases or vocabulary used to describe a particular data type or subject area)
3.由于syntax没有定义变量与数学公式代表的意思，以及它们如何产生的等原因，致使很多重要的semantic信息被model忽略了，再加上semantic文本描述二义性等等导致了一堆缺点。因此，semantic should be defined independently of the standard formats used for model encoding(semantic应该独立于syntax定义，大概意思是)。怎么定义，怎么encode？ontology！
本文介绍三种ontology，应用于不同的model的环节，SBO很成熟，KISAO上升比较快，TEDDY处于初期
Model Structure: SBO
SBO describes entities used in computational modeling. Annotating entities with SBO terms allows for unambiguous and explicit understanding of the meaning of these entities.
SBO is composed of seven vocabulary branches
physical entity:分为function entity(代谢entity), material entity(高分子，简单化合物)
participant role: entity在建模过程中扮演的role，如催化剂，基底
modeling framework：没太懂
Occurring entity representation: 生化过程，事件的类型，physical entity的processual关系。分为两个branch，process branch表示生化过程的类型，如卵裂，异构化。relationship branch表示加在生化过程上的control，如刺激，抑制，催化。
System description parameter: 定义了定量描述生化过程所用的参数，如希尔系数等等。
mathematical exp: 对描述生化过程所用的数学结构进行分类（Briggs—Haldane rate law 用MathML编写存储）
Metadata representation：描述了一些加到model中不改变model行为以及meaning的信息
Simulation Procedure: KiSAO
SBO给formal representation提供了semantic layer，但是formal representation没有提供simulation procedure的信息，用不同simulation procedure algorithm在model上会有不同的结果，同时也不是所有algorithm都能用。KiSAO就是用来Describing simulation algorithms的。
KiSAO有3个branch
simulation algorithm，this branch is a hierarchically structured. 后裔算法是由它的祖先算法推导出来的
Characteristic branch: 包括model与numerical kinetic的特点，前者是how the model can be simulated(离散or连续)，后者是system behavior(确定or随机)以及timestep的特点
parameter branch：algorithm所用的参数
algorithm in KiSAO is linked to characteristics, so characteristic based algorithm classification can be developed. Therefore, KiSAO is an ontology to define algorithms suitable for use within a given simulation setup(给我simulation所需要的条件，我就可以用KiSAO找到对应的algorithm)
剩余段落内容见文章
Numerical Results: TEDDY
我们要做的是模拟用计算机模拟biological experiment. We have a computational model(semantically enriched by SBO), and recipe of producing a simulation experiment(using KiSAO), 我们现在要的是对simulation experiment behavior的描述，且这个描述要systematic以及machine readable（现有free text描述没法达到这个要求），所以我们就用TEDDY。
TEDDY有4个branch
Temporal behavior: describe the way a system changes with the respect to some aspect of the environment
behavior characteristic: temporal behavior的属性
behavior diversification: the way one or several temporal behaviors are modified or related upon the interaction with information external to the system.
functional motif: structures of a submodel that may generate temporal behaviors.