BIND - a data specification for storing and describing biomolecular interactions, molecular complexes and pathways
BIND - a data specification for storing and describing biomolecular interactions, molecular complexes and pathways
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DOI：
10.1093/bioinformatics/16.5.465
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发表时间：
2000-05-01
期刊：
影响因子：
5.8
通讯作者：
Hogue, CWV
中科院分区：
文献类型：
--
作者：
Bader, GD;Hogue, CWV
动机：蛋白质组学正朝着高通量方法迈进，以识别和表征细胞中所有蛋白质，蛋白质结构域和蛋白质相互作用，并最终将创建比人类基因组项目更具记录的生物学信息。在细胞中表达的每种蛋白质在其功能过程中都可以与其他各种蛋白质和分子相互作用。需要标准的数据规范，该规范可以在其所有细节中描述和存储这些信息，并允许数据的有效跨平台传输。完整的规范必须是用于管理和分析此信息的任何数据库或工具的基础：我们已经在ASN.1中定义了一个完整的数据规范，该数据规范可以描述有关生物分子相互作用，复合物和路径的信息。我们的小组正在数据库中使用此数据规范，即生物分子交互网络数据库（BIND）。交互记录基于两个对象之间的相互作用。物体可以是蛋白质，DNA，RNA，配体，分子或相互作用。相互作用描述包括用于观察相互作用，保守序列，分子位置，化学作用，动力学，热力学和化学状态的相互作用，保守序列，分子位置，化学能力和化学状态的相互作用条件。分子复合物被定义为形成复杂的两个以上相互作用的集合，并具有额外的描述性信息，例如复杂的拓扑结构。途径被定义为具有两个以上相互作用的集合，并具有其他描述性信息，例如细胞周期阶段。提出人类可读的扁平文件格式的提议请求，该格式反映了绑定数据规范的要求。可利用的各方。 .mshri.on.ca/pub/bind/spec/bind.asn。可以通过我们的主页http://bioinfo.mshri.ca/bind/asn-browser/.contact：hogue @ mshri.on.ca来获得此文档的交互式浏览器。
Motivation: Proteomics is gearing up towards high-throughput methods for identifying and characterizing all of the proteins, protein domains and protein interactions in a cell and will eventually create more recorded biological information than Human Genome Project. Each protein expressed in a cell can interact with various other proteins and molecules in the course of its function. A standard data specification is required that can describe and store this information in all its detail and allow efficient cross-platform transfer of data. A complete specification must be the basis for any database or tool for managing and analysing this information.Results: We have defined a complete data specification in ASN.1 that can describe information about biomolecular interactions, complexes and pathways. Our group is using this data specification in our database, the Biomolecular Interaction Network Database (BIND). An interaction record is based on the interaction between two objects. An object can be a protein, DNA, RNA, ligand, molecular or an interaction. Interaction description encompasses cellular location experimental conditions used to observe the interaction, conserved sequence, molecular location, chemical action, kinetics, thermodynamics, and chemical state. Molecular complexes are defined as collections of more than two interactions that form a complex, with extra descriptive information such as complex topology. Pathways are defined as collections of more than two interactions that forma pathway, with additional descriptive information such as cell cycle stage. A request for proposal of a human readable flat-file format that mirrors the BIND data specification is also tendered for interested parties.Availability: The ASN.1 data specification for biomolecular interaction, molecular complex and pathway data is available at ftp://bioinfo.mshri.on.ca/pub/BIND/Spec/bind.asn. An interactive browser for this document is available through our homepage at http://bioinfo.mshri.on.ca/BIND/asn-browser/.Contact: hogue @ mshri.on.ca.