Reactome graph database: Efficient access to complex pathway data.
Reactome graph database: Efficient access to complex pathway data.
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DOI：
10.1371/journal.pcbi.1005968
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发表时间：
2018-01
影响因子：
4.3
通讯作者：
Hermjakob H
中科院分区：
文献类型：
--
作者：
Fabregat A;Korninger F;Viteri G;Sidiropoulos K;Marin-Garcia P;Ping P;Wu G;Stein L;D'Eustachio P;Hermjakob H
Reactome是一个免费，开源，开放数据，策划和同行评审的生物分子途径知识库。其主要优先事项之一是提供轻松有效的访问其高质量的策展数据。目前，生物途径数据库通常将其内容存储在关系数据库中。这限制了访问效率，因为存在与遍历高度互连的数据的查询相关联的性能问题。可以更有效地查询图形数据库中的相同数据。在这里，我们介绍了采用图形数据库（Neo4j）以及提供对这些数据的访问的新ContentService（REST API）的基本原理。Neo4j图形数据库及其查询语言Cypher提供了对复杂Reactome数据模型的有效访问，便于轻松遍历和知识发现。该技术的采用大大提高了查询效率，平均查询时间减少了93%。构建在图形数据库之上的Web服务通过面向对象的查询提供对Reactome数据的编程访问，但也支持利用新的基于图形的底层数据存储的更复杂的查询。通过采用图形数据库技术，我们为社区提供了一个高性能的路径数据资源。Reactome图数据库用例展示了NoSQL数据库引擎在复杂生物数据类型中的强大功能。为了更好地支持基因组分析，建模，系统生物学和教育，我们现在提供生物分子途径的知识库作为图形数据库。我们已经开发了一个工具，用于在每个季度发布过程中将Reactome内容从策展中使用的关系数据库迁移到图形数据库。新的图形数据库有两个主要优点：更高的性能和更简单的方式来执行复杂的查询。Reactome已经调整了其软件基础设施，以从这种日益流行的存储技术中受益，通过将平均查询时间减少93%，显着提高查询效率。我们坚信，Reactome成功采用图形数据库表明了这项新技术可能在该领域产生的积极影响，并可以为其他具有类似复杂数据模型的社区项目提供一个实际示例，将其存储迁移到图形数据库，同时保留其数据模型。
Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. One of its main priorities is to provide easy and efficient access to its high quality curated data. At present, biological pathway databases typically store their contents in relational databases. This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data. The same data in a graph database can be queried more efficiently. Here we present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data. The Neo4j graph database and its query language, Cypher, provide efficient access to the complex Reactome data model, facilitating easy traversal and knowledge discovery. The adoption of this technology greatly improved query efficiency, reducing the average query time by 93%. The web service built on top of the graph database provides programmatic access to Reactome data by object oriented queries, but also supports more complex queries that take advantage of the new underlying graph-based data storage. By adopting graph database technology we are providing a high performance pathway data resource to the community. The Reactome graph database use case shows the power of NoSQL database engines for complex biological data types. To better support genome analysis, modeling, systems biology and education, we now offer our knowledgebase of biomolecular pathways as a graph database. We have developed a tool to migrate the Reactome content from the relational database used in curation to a graph database during each quarterly release process. The new graph database has two main advantages; higher performance and simpler ways to perform complex queries. Reactome has already adapted its software infrastructure to benefit from this growing in popularity storage technology, significantly improving query efficiency, by reducing the average query time by 93%. We strongly believe that the successful adoption of a graph database by Reactome demonstrates the positive impact this new technology could potentially have in the field and could provide a practical example for other community projects with similar complex data models to move their storage to a graph database while retaining their data models.
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影响因子：
3
作者：
Toure, Vasundra;Mazein, Alexander;Auffray, Charles
通讯作者：
Auffray, Charles
影响因子：
4.5
作者：
Lysenko A;Roznovăţ IA;Saqi M;Mazein A;Rawlings CJ;Auffray C
通讯作者：
Auffray C
影响因子：
14.9
作者：
Birney, E;Andrews, D;Hubbard, T
通讯作者：
Hubbard, T
DOI：
10.1093/bioinformatics/btv460
发表时间：
2015-12-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Summer G;Kelder T;Ono K;Radonjic M;Heymans S;Demchak B
通讯作者：
Demchak B
Reactome：生物学途径和过程的知识库。
影响因子：
12.3
作者：
Vastrik, Imre;D'Eustachio, Peter;Schmidt, Esther;Joshi-Tope, Geeta;Gopinath, Gopal;Croft, David;de Bono, Bernard;Gillespie, Marc;Jassal, Bijay;Lewis, Suzanna;Matthews, Lisa;Wu, Guanming;Birney, Ewan;Stein, Lincoln
通讯作者：
Stein, Lincoln