Linking data with Identifiers.org

将数据与 Identifiers.org 链接

• 批准号: BB/K016946/1
• 负责人: Henning Hermjakob
• 金额: $ 15.22万
• 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: 2013
• 资助国家: 英国
• 起止时间: 2013 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FK016946%2F1
• 关键词: Linking; data; Identifiers.org

Annotating data, life science datasets with cross-references to other sources of knowledge has always be very important. These metadata are often what separate valuable information from heaps of unusable data. With the advent of systems biology, the size and complexity of datasets shifted the balance from direct human interaction to automated computer processing. Such operations are greatly facilitated if the metadata is encoded following standard procedures and using controlled vocabularies. If those procedures and vocabularies are shared between different types of data, it becomes possible to align, compare and integrate different datasets. A key part of any cross-reference is the identifier of the resource it points to. This identifier must be unique, perennial, resolvable and free. Most data providers create identifiers for their own records; for example '9606' identifies 'Homo sapiens' in the Taxonomy, and '22140103' identifies the latest publication about Identifiers.org in PubMed. However, those identifiers are only unique within a given dataset so their usefulness is limited when considering records in a wider context.Identifiers.org provides such global identifiers, and resolves them to the relevant dataset. In order to achieve this purpose, it uses the information recorded in the MIRIAM Registry (http://www.ebi.ac.uk/miriam/). Therefore both projects provide a distinct part of the final technical solution. Identifiers generated with the Registry make use of the accession numbers supplied by data providers, but also contain information about the collection they come from. All identifiers are unique, resolvable and robust. They allow persons or software tools to directly access the identified pieces of data on the web, via alternative providers. Although a prototype, Identifiers.org has been adopted by a number of communities and projects, as it fulfils their need for perennial cross-references and removes their previous need for maintaining and keeping up to date long lists of ever changing web links (or URLs).As more and more communities realise the benefits of using Identifiers.org URIs, new needs and use cases have appeared. This proposal seeks to strengthen and extend the services provided by the resource in order to respond to those new user requests. We will make the resource easier to use in automated procedures, specially for semantic web applications. This involves providing the content of the Registry in Resource Description Framework (RDF) format and supply a SPARQL endpoint for query purposes. Users will be able to fine-tuned the way identifiers are resolved, via the creation of 'profiles', that will record their preferences. The resource will allow the communities (more specially the data providers themselves) to get involved in the maintenance of the Registry. This will take place via a system of "ownership" by data providers of their record in the Registry. Although we currently have automatic systems in place to detect obsolete information, having the actual data providers contributing to the maintenance would ensure better quality of the recorded information, meaning a better quality of the services provided. Finally we will improve and extend the underlying computing infrastructure. By deploying it in more more data centres, we will provide more reliable services to an ever growing number of users.The resulting resource will provide a way to seamlessly link all data annotated with the same URI to represent the same concept, a key step towards data integration. By providing a semantic glue between those datasets, Identifiers.org will facilitate data retrieval, comparison, integration, locally or through the semantic web. It will also facilitate the reasoning on the integrated datasets and lead to new, possibly automated discovery in the biomedical domain.

注释数据，生命科学数据集与其他知识来源的交叉引用一直非常重要。这些元数据通常是将有价值的信息与大量无用的数据分开的东西。随着系统生物学的出现，数据集的规模和复杂性将平衡从直接的人类交互转移到自动化计算机处理。如果元数据遵循标准过程并使用受控词汇表进行编码，则会极大地促进此类操作。如果这些程序和词汇表在不同类型的数据之间共享，就有可能调整、比较和整合不同的数据集。任何交叉引用的关键部分都是它所指向的资源的标识符。这个标识符必须是唯一的、永久的、可解析的和自由的。大多数数据提供商都会为自己的记录创建标识符;例如，“9606”标识分类中的“智人”，“22140103”标识PubMed中有关Identifiers.org的最新出版物。然而，这些标识符仅在给定的数据集中是唯一的，因此当考虑更广泛的www.example.com中的记录时，它们的有用性是有限context.Identifiers.org提供了这样的全局标识符，并将它们解析为相关的数据集。为了实现这一目的，它使用MIRIAM登记处（http：//www.ebi.ac.uk/miriam/）中记录的信息。因此，这两个项目提供了最终技术解决方案的不同部分。登记处生成的标识符使用数据提供者提供的登录号，但也包含有关其来源的集合的信息。所有标识符都是唯一的、可解析的和鲁棒的。它们允许个人或软件工具通过替代提供商直接访问网络上已识别的数据。虽然只是一个原型，但Identifiers.org已经被许多社区和项目所采用，因为它满足了他们对常年交叉引用的需求，并消除了他们以前对维护和保持不断变化的Web链接（或URL）的最新长列表的需求。随着越来越多的社区意识到使用Identifiers.org URI的好处，新的需求和用例已经出现。这项提议旨在加强和扩大该资源提供的服务，以满足这些新用户的要求。我们将使资源更容易在自动化过程中使用，特别是语义Web应用程序。这涉及到以资源描述框架（RDF）格式提供注册表的内容，并提供一个SPARQL端点用于查询目的。用户将能够通过创建“配置文件”来微调标识符的解析方式，该配置文件将记录他们的偏好。该资源将使各社区（更具体地说是数据提供者本身）能够参与登记册的维护工作。这将通过数据提供者对其在登记册中的记录的“所有权”制度来实现。虽然我们目前有自动系统来检测过时的信息，但让实际的数据提供者参与维护将确保记录的信息质量更高，这意味着提供的服务质量更高。最后，我们将改进和扩展底层计算基础设施。通过在更多的数据中心部署它，我们将为越来越多的用户提供更可靠的服务。由此产生的资源将提供一种无缝链接所有使用相同URI注释的数据的方法，以表示相同的概念，这是迈向数据集成的关键一步。通过在这些数据集之间提供语义粘合剂，Identifiers.org将促进本地或通过语义网的数据检索、比较、集成。它还将促进对综合数据集的推理，并在生物医学领域带来新的、可能是自动化的发现。

项目成果

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

• DOI: 10.1186/2041-1480-5-5
• 发表时间: 2014-02-05
• 期刊: Journal of biomedical semantics
• 影响因子: 1.9
• 作者: Katayama T;Wilkinson MD;Aoki-Kinoshita KF;Kawashima S;Yamamoto Y;Yamaguchi A;Okamoto S;Kawano S;Kim JD;Wang Y;Wu H;Kano Y;Ono H;Bono H;Kocbek S;Aerts J;Akune Y;Antezana E;Arakawa K;Aranda B;Baran J;Bolleman J;Bonnal RJ;Buttigieg PL;Campbell MP;Chen YA;Chiba H;Cock PJ;Cohen KB;Constantin A;Duck G;Dumontier M;Fujisawa T;Fujiwara T;Goto N;Hoehndorf R;Igarashi Y;Itaya H;Ito M;Iwasaki W;Kalaš M;Katoda T;Kim T;Kokubu A;Komiyama Y;Kotera M;Laibe C;Lapp H;Lütteke T;Marshall MS;Mori T;Mori H;Morita M;Murakami K;Nakao M;Narimatsu H;Nishide H;Nishimura Y;Nystrom-Persson J;Ogishima S;Okamura Y;Okuda S;Oshita K;Packer NH;Prins P;Ranzinger R;Rocca-Serra P;Sansone S;Sawaki H;Shin SH;Splendiani A;Strozzi F;Tadaka S;Toukach P;Uchiyama I;Umezaki M;Vos R;Whetzel PL;Yamada I;Yamasaki C;Yamashita R;York WS;Zmasek CM;Kawamoto S;Takagi T
• 通讯作者: Takagi T

BioModels: Content, Features, Functionality, and Use.

• DOI: 10.1002/psp4.3
• 发表时间: 2015-02
• 期刊: CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY
• 影响因子: 3.5
• 作者: Juty, N;Ali, R;Glont, M;Keating, S;Rodriguez, N;Swat, M J;Wimalaratne, S M;Hermjakob, H;Le Novere, N;Laibe, C;Chelliah, V
• 通讯作者: Chelliah, V

BioModels: ten-year anniversary.

• DOI: 10.1093/nar/gku1181
• 发表时间: 2015-01
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Chelliah V;Juty N;Ajmera I;Ali R;Dumousseau M;Glont M;Hucka M;Jalowicki G;Keating S;Knight-Schrijver V;Lloret-Villas A;Natarajan KN;Pettit JB;Rodriguez N;Schubert M;Wimalaratne SM;Zhao Y;Hermjakob H;Le Novère N;Laibe C
• 通讯作者: Laibe C

SPARQL-enabled identifier conversion with Identifiers.org.

• DOI: 10.1093/bioinformatics/btv064
• 发表时间: 2015-06-01
• 期刊: Bioinformatics (Oxford, England)
• 作者: Wimalaratne SM;Bolleman J;Juty N;Katayama T;Dumontier M;Redaschi N;Le Novère N;Hermjakob H;Laibe C
• 通讯作者: Laibe C

BioModels linked dataset.

• DOI: 10.1186/s12918-014-0091-5
• 发表时间: 2014-08-15
• 期刊: BMC systems biology
• 作者: Wimalaratne SM;Grenon P;Hermjakob H;Le Novère N;Laibe C
• 通讯作者: Laibe C