Software infrastructure to support the standard of model curation and annotation MIRIAM

支持模型管理和注释 MIRIAM 标准的软件基础设施

• 批准号: BB/E006248/1
• 负责人: Nicolas Le Novere
• 金额: $ 10.55万
• 依托单位: European Bioinformatics Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2006
• 资助国家: 英国
• 起止时间: 2006 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FE006248%2F1
• 关键词: Software; infrastructure; support; standard; model

Systems Biology recently emerged as on of main field in life sciences. A crucial component of this discipline is the development of quantitative models to simulate the biological processes. Scientists need to store and exchange those models to leverage on each-other expertise and production. A prerequisite is the standardisation of model's syntax and content. In collaboration with the community of modellers and developers, we developed a standard, MIRIAM, that precises what mandatory information authors have to add to a quantitative model in order to facilitate its understanding by other scientists. MIRIAM is made up of two parts: 1) a set of rules controlling the correspondance between the model and its description in the scientific literature; 2) A set of annotation describing the generation of the model, and documenting each of its elements. For MIRIAM to be effectively adopted, we need to provide the computing resources necessary to its implementation. We will build a database of officialy endorsed data resources. This database will provide for each data resource all the details necessary to the implementation of the standard. We will develop a simple interface to facilitate the automatic access to the database. Software libraries will be provided to implement the access to the interface and to facilitate the development of third party software. In collaboration with the California Institute of Technology and the Bioengineering Institute of Auckland we will work to expand the support of the standard MIRIAM by the modelling languages SBML and CellML. This will allow a significant fraction of modelling tools to produce MIRIAM-compliant models. The endorsement of public standards by scientists, developers and publishers will be a crucial step toward the effective storage, exchange and reuse of quantitative models in Biology, one of the cornerstone of Systems Biology. The wide acceptance of MIRIAM will only be achieved through the availability of easy to use supporting softwares and resources such as those presented in this project.

系统生物学是近年来兴起的生命科学的主要领域之一.这门学科的一个重要组成部分是发展定量模型来模拟生物过程。科学家需要存储和交换这些模型，以利用彼此的专业知识和生产。一个先决条件是模型语法和内容的标准化。在与建模者和开发人员社区的合作中，我们开发了一个标准MIRIAM，该标准精确规定了作者必须添加到定量模型中的强制性信息，以促进其他科学家的理解。MIRIAM由两部分组成：1）一组规则，控制模型与科学文献中的描述之间的对应关系; 2）一组注释，描述模型的生成，并记录其每个元素。为了有效采用MIRIAM，我们需要提供其实施所需的计算资源。我们将建立一个官方认可的数据资源库。该数据库将为每个数据源提供执行标准所需的所有详细信息。我们将开发一个简单的界面，以方便自动访问数据库。将提供软件库，以实现对界面的访问，并促进第三方软件的开发。我们将与加州理工学院和奥克兰生物工程学院合作，通过建模语言SBML和CellML扩展对标准MIRIAM的支持。这将使很大一部分建模工具能够产生符合MIRIAM的模型。科学家、开发人员和出版商对公共标准的认可将是生物学中定量模型有效存储、交换和重用的关键一步，生物学是系统生物学的基石之一。只有通过提供易于使用的支持软件和资源（如本项目中提供的软件和资源），才能广泛接受MIRIAM。

项目成果

Retrieval, alignment, and clustering of computational models based on semantic annotations.

• DOI: 10.1038/msb.2011.41
• 发表时间: 2011-07-19
• 期刊: Molecular systems biology
• 影响因子: 9.9

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.

• DOI: 10.1371/journal.pbio.2001414
• 发表时间: 2017-06
• 期刊: PLoS biology
• 影响因子: 9.8
• 作者: McMurry JA;Juty N;Blomberg N;Burdett T;Conlin T;Conte N;Courtot M;Deck J;Dumontier M;Fellows DK;Gonzalez-Beltran A;Gormanns P;Grethe J;Hastings J;Hériché JK;Hermjakob H;Ison JC;Jimenez RC;Jupp S;Kunze J;Laibe C;Le Novère N;Malone J;Martin MJ;McEntyre JR;Morris C;Muilu J;Müller W;Rocca-Serra P;Sansone SA;Sariyar M;Snoep JL;Soiland-Reyes S;Stanford NJ;Swainston N;Washington N;Williams AR;Wimalaratne SM;Winfree LM;Wolstencroft K;Goble C;Mungall CJ;Haendel MA;Parkinson H
• 通讯作者: Parkinson H

MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology.

Miriam Resources：生成和解决系统生物学中强大的交叉引用的工具。

• DOI: 10.1186/1752-0509-1-58
• 发表时间: 2007-12-13
• 期刊: BMC SYSTEMS BIOLOGY
• 作者: Laibe, Camille;Le Novere, Nicolas
• 通讯作者: Le Novere, Nicolas

Ranked retrieval of Computational Biology models.

• DOI: 10.1186/1471-2105-11-423
• 发表时间: 2010-08-11
• 期刊: BMC bioinformatics
• 影响因子: 3
• 作者: Henkel R;Endler L;Peters A;Le Novère N;Waltemath D
• 通讯作者: Waltemath D

The EBI RDF platform: linked open data for the life sciences.

• DOI: 10.1093/bioinformatics/btt765
• 发表时间: 2014-05-01
• 期刊: Bioinformatics (Oxford, England)
• 作者: Jupp S;Malone J;Bolleman J;Brandizi M;Davies M;Garcia L;Gaulton A;Gehant S;Laibe C;Redaschi N;Wimalaratne SM;Martin M;Le Novère N;Parkinson H;Birney E;Jenkinson AM
• 通讯作者: Jenkinson AM