BioModels.net Web Services, a free and integrated toolkit for computational modelling software
BioModels.net Web Services, a free and integrated toolkit for computational modelling software
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DOI：
10.1093/bib/bbp056
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发表时间：
2010-05-01
影响因子：
9.5
通讯作者：
Laibe, Camille
中科院分区：
文献类型：
--
作者：
Li, Chen;Courtot, Melanie;Laibe, Camille
交换和分享科学成果对计算建模领域的研究人员来说是必不可少的。net为模型管理定义了公认的标准。MIRIAM（模型注释中要求的最小信息）是生物学中定量模型的注释和管理过程的标准。为了支持这个标准，MIRIAM Resources维护了一组用于注释模型的标准数据类型，并提供了用于操作这些注释的服务。此外，BioModels.net创建了受控词汇表，例如SBO（系统生物学本体），它严格索引、定义和链接系统生物学中使用的术语。最后，biommodels Database提供了一个免费的、集中的、可公开访问的数据库，用于存储、搜索和检索经过整理和注释的计算模型。每个资源都提供了一个web界面来提交、搜索、检索和显示其数据。此外，BioModels.net团队提供了一组Web服务，允许社区以编程方式访问资源。然后，用户可以执行远程查询，例如检索模型并解析其所有MIRIAM annotation，以及获取有关相关SBO术语的详细信息。这些web服务使用已建立的标准。通信依赖于SOAP（简单对象访问协议）消息，可用的查询在WSDL （Web服务描述语言）文件中进行描述。为了简化客户端软件的开发，提供了几个库。通过允许研究人员在他们自己的工具中检索生物模型，在工作流程中组合查询并有效地分析模型，BioModels.net Web Services使研究人员在模拟和理解整个生物系统方面又向前迈进了一步。
Exchanging and sharing scientific results are essential for researchers in the field of computational modelling. BioModels.net defines agreed-upon standards for model curation. A fundamental one, MIRIAM (Minimum Information Requested in the Annotation of Models), standardises the annotation and curation process of quantitative models in biology. To support this standard, MIRIAM Resources maintains a set of standard data types for annotating models, and provides services for manipulating these annotations. Furthermore, BioModels.net creates controlled vocabularies, such as SBO (Systems Biology Ontology) which strictly indexes, defines and links terms used in Systems Biology. Finally, BioModels Database provides a free, centralised, publicly accessible database for storing, searching and retrieving curated and annotated computational models. Each resource provides a web interface to submit, search, retrieve and display its data. In addition, the BioModels.net team provides a set of Web Services which allows the community to programmatically access the resources. A user is then able to perform remote queries, such as retrieving a model and resolving all its MIRIAM Annotations, as well as getting the details about the associated SBO terms. These web services use established standards. Communications rely on SOAP (Simple Object Access Protocol) messages and the available queries are described in a WSDL (Web Services Description Language) file. Several libraries are provided in order to simplify the development of client software. BioModels.net Web Services make one step further for the researchers to simulate and understand the entirety of a biological system, by allowing them to retrieve biological models in their own tool, combine queries in workflows and efficiently analyse models.