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RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis.
Database: The Journal of Biological Databases and Curation ( IF 5.8 ) Pub Date : 2020-01-01 , DOI: 10.1093/database/baaa017
Vidisha Singh 1 , George D Kalliolias 2, 3 , Marek Ostaszewski 4 , Maëva Veyssiere 1 , Eleftherios Pilalis 5 , Piotr Gawron 4 , Alexander Mazein 4 , Eric Bonnet 6 , Elisabeth Petit-Teixeira 1 , Anna Niarakis 1
Affiliation  

Rheumatoid arthritis (RA) is a progressive, inflammatory autoimmune disease of unknown aetiology. The complex mechanism of aetiopathogenesis, progress and chronicity of the disease involves genetic, epigenetic and environmental factors. To understand the molecular mechanisms underlying disease phenotypes, one has to place implicated factors in their functional context. However, integration and organization of such data in a systematic manner remains a challenging task. Molecular maps are widely used in biology to provide a useful and intuitive way of depicting a variety of biological processes and disease mechanisms. Recent large-scale collaborative efforts such as the Disease Maps Project demonstrate the utility of such maps as versatile tools to organize and formalize disease-specific knowledge in a comprehensive way, both human and machine-readable. We present a systematic effort to construct a fully annotated, expert validated, state-of-the-art knowledge base for RA in the form of a molecular map. The RA map illustrates molecular and signalling pathways implicated in the disease. Signal transduction is depicted from receptors to the nucleus using the Systems Biology Graphical Notation (SBGN) standard representation. High-quality manual curation, use of only human-specific studies and focus on small-scale experiments aim to limit false positives in the map. The state-of-the-art molecular map for RA, using information from 353 peer-reviewed scientific publications, comprises 506 species, 446 reactions and 8 phenotypes. The species in the map are classified to 303 proteins, 61 complexes, 106 genes, 106 RNA entities, 2 ions and 7 simple molecules. The RA map is available online at ramap.elixir-luxembourg.org as an open-access knowledge base allowing for easy navigation and search of molecular pathways implicated in the disease. Furthermore, the RA map can serve as a template for omics data visualization.

中文翻译:

RA-map:构建最先进的类风湿关节炎交互式知识库。

类风湿性关节炎(RA)是一种病因不明的进行性炎症性自身免疫性疾病。该疾病的发病机制、进展和慢性的复杂机制涉及遗传、表观遗传和环境因素。为了了解疾病表型背后的分子机制,我们必须将相关因素置于其功能背景中。然而,以系统的方式整合和组织这些数据仍然是一项具有挑战性的任务。分子图谱广泛应用于生物学中,为描述各种生物过程和疾病机制提供了有用且直观的方式。最近的大规模协作工作(例如疾病地图项目)证明了此类地图作为多功能工具的实用性,可以以人类和机器可读的综合方式组织和形式化特定疾病的知识。我们提出了系统性的努力,以分子图谱的形式构建一个完全注释的、经过专家验证的、最先进的 RA 知识库。RA 图谱说明了与该疾病有关的分子和信号传导途径。使用系统生物学图形符号 (SBGN) 标准表示法描述从受体到细胞核的信号转导。高质量的手动管理、仅使用针对人类的研究并专注于小规模实验,旨在限制地图中的误报。最先进的 RA 分子图谱使用了 353 份同行评审的科学出版物的信息,包括 506 个物种、446 个反应和 8 种表型。图中的物种分为 303 个蛋白质、61 个复合物、106 个基因、106 个 RNA 实体、2 个离子和 7 个简单分子。RA 图谱可在 ramap.elixir-luxembourg.org 上在线获取,作为开放获取的知识库,可以轻松导航和搜索与该疾病有关的分子途径。此外,RA 图可以作为组学数据可视化的模板。
更新日期:2020-04-20
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