Karp P D
Bioinformatics Research Group, SRI International, EK223, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA.
Bioinformatics. 2000 Mar;16(3):269-85. doi: 10.1093/bioinformatics/16.3.269.
A number of important bioinformatics computations involve computing with function: executing computational operations whose inputs or outputs are descriptions of the functions of biomolecules. Examples include performing functional queries to sequence and pathway databases, and determining functional equality to evaluate algorithms that predict function from sequence. A prerequisite to computing with function is the existence of an ontology that provides a structured semantic encoding of function. Functional bioinformatics is an emerging subfield of bioinformatics that is concerned with developing ontologies and algorithms for computing with biological function.
The article explores the notion of computing with function, and explains the importance of ontologies of function to bioinformatics. The functional ontology developed for the EcoCyc database is presented. This ontology can encode a diverse array of biochemical processes, including enzymatic reactions involving small-molecule substrates and macromolecular substrates, signal-transduction processes, transport events, and mechanisms of regulation of gene expression. The ontology is validated through its use to express complex functional queries for the EcoCyc DB.
许多重要的生物信息学计算涉及函数计算，即执行输入或输出为生物分子功能描述的计算操作。示例包括对序列和通路数据库进行功能查询，以及确定功能等效性以评估从序列预测功能的算法。函数计算的一个先决条件是存在一个提供功能结构化语义编码的本体。功能生物信息学是生物信息学中一个新兴的子领域，致力于开发用于生物功能计算的本体和算法。
本文探讨了函数计算的概念，并解释了功能本体对生物信息学的重要性。介绍了为EcoCyc数据库开发的功能本体。该本体可以编码各种生化过程，包括涉及小分子底物和大分子底物的酶促反应、信号转导过程、转运事件以及基因表达调控机制。通过使用该本体为EcoCyc数据库表达复杂的功能查询来验证该本体。
