Global biotic interactions: An open infrastructure to share and analyze species-interaction datasets
Global biotic interactions: An open infrastructure to share and analyze species-interaction datasets
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DOI：
10.1016/j.ecoinf.2014.08.005
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发表时间：
2014-11-01
影响因子：
5.1
通讯作者：
Mungall, Chris J.
中科院分区：
文献类型：
--
作者：
Poelen, Jorrit H.;Simons, James D.;Mungall, Chris J.
生物与其环境之间错综复杂的相互作用网络形成了维持地球上生命的生态系统。通过对这些相互作用的详细了解，生态学家和生物学家可以更好地预测不同环境因素对生态系统的影响。尽管有大量关于生物和非生物相互作用的研究数据，但没有跨越分类学、地理空间和时间域的全面和容易获得的数据收集。生物交互数据集是有效的孤岛，抑制了跨数据集的比较。为了汇集资源并揭示单个数据集，需要专门的研究工具来聚合、规范化现有数据集并将其与标准分类法、本体、词汇表和结构化数据存储库集成。全球生物相互作用（GloBI）通过一个开放的、社区驱动的基础设施提供了这样的工具，旨在降低研究人员进行生态系统分析和建模的障碍。GloBI提供了一种工具，它（a）摄取、规范化和聚合数据集，（B）将可互操作的数据与公认的本体（例如，OBO关系本体、Uberon和环境本体）、词汇表（例如，沿海和海洋生态分类标准）和分类学（例如，综合分类信息系统和国家生物技术信息中心分类数据库），（c）通过应用程序编程接口（API）和各种数据档案（达尔文核心、海龟和Neo4j）提供数据，（d）收集了约50 000个分类群中约700 000个物种相互作用的数据，涵盖来自19个数据源的1 100多个参考文献。GloBI采取了开源和开放数据的方法，以使综合物种相互作用数据最大限度地可访问，并鼓励用户提供反馈，贡献数据，并改进数据访问方法。GloBI收集的数据集目前用于生命百科全书（EOL）和墨西哥湾物种相互作用（GoMexSI）。(C)2014作者由爱思唯尔公司出版
An intricate network of interactions between organisms and their environment form the ecosystems that sustain life on earth. With a detailed understanding of these interactions, ecologists and biologists can make better informed predictions about the ways different environmental factors will impact ecosystems. Despite the abundance of research data on biotic and abiotic interactions, no comprehensive and easily accessible data collection is available that spans taxonomic, geospatial, and temporal domains. Biotic-interaction datasets are effectively siloed, inhibiting cross-dataset comparisons. In order to pool resources and bring to light individual datasets, specialized research tools are needed to aggregate, normalize, and integrate existing datasets with standard taxonomies, ontologies, vocabularies, and structured data repositories. Global Biotic Interactions (GloBI) provides such tools by way of an open, community-driven infrastructure designed to lower the barrier for researchers to perform ecological systems analysis and modeling. GloBI provides a tool that (a) ingests, normalizes, and aggregates datasets, (b) integrates interoperable data with accepted ontologies (e.g., OBO Relations Ontology, Uberon, and Environment Ontology), vocabularies (e.g., Coastal and Marine Ecological Classification Standard), and taxonomies (e.g., Integrated Taxonomic Information System and National Center for Biotechnology Information Taxonomy Database), (c) makes data accessible through an application programming interface (API) and various data archives (Darwin Core, Turtle, and Neo4j), and (d) houses a data collection of about 700,000 species interactions across about 50,000 taxa, covering over 1100 references from 19 data sources. GloBI has taken an open-source and open-data approach in order to make integrated species-interaction data maximally accessible and to encourage users to provide feedback, contribute data, and improve data access methods. The GloBI collection of datasets is currently used in the Encyclopedia of Life (EOL) and Gulf of Mexico Species Interactions (GoMexSI). (C) 2014 The Authors. Published by Elsevier B.V.