通过网络接口和网络服务编程使用 EMBL-EBI 服务。

Fábio Madeira, Nandana Madhusoodanan, Joonheung Lee, Alberto Eusebi, Ania Niewielska, Adrian R. N. Tivey, Stuart Meacham, Rodrigo Lopez, Sarah Butcher
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引用次数: 0

摘要

欧洲生物信息学研究所(EMBL-EBI)的 "工作分配器"(Job Dispatcher)框架提供了对生物信息学中至关重要的各种核心数据库和分析工具的访问。除了提供这些资源的网络接口外,还提供了使用 REST 和 SOAP 协议的网络服务,可以进行编程访问,并将其集成到其他应用程序和分析工作流和管道中。本文介绍了可供研究人员和生物信息学家选择的各种方案,他们可以通过使用 Perl、Python 和 Java 提供的 RESTful 网络服务客户端的网络接口使用我们的资源,也可以使用 Docker 容器将资源整合到分析管道和工作流程中。© 2024 作者。当前协议》由 Wiley Periodicals LLC 出版。基本协议 1:使用 Dbfetch 通过网络接口从 EMBL-EBI 检索数据 替代协议 1:使用 WSDbfetch 通过 REST 接口从 EMBL-EBI 检索数据 替代协议 2:使用 Dbfetch 通过带有 Python 客户端的 RESTful 网络服务从 EMBL-EBI 检索数据 支持协议 1:安装 Python REST 网络服务客户端 基本协议 2:使用 FBF 检索序列相似性通过 Web 界面使用 FASTA 搜索进行序列相似性搜索 替代协议 3:使用 Perl 客户端通过 RESTful 网络服务使用 FASTA 进行序列相似性搜索 支持协议 2:安装 Perl RESTful 网络服务客户端 基本协议 3:使用 Python 客户端通过 NCBI BLAST+ RESTful 网络服务进行序列相似性搜索 基本协议 4:使用 Hibernate 数据库进行序列相似性搜索 支持协议 1:安装 Python RESTful 网络服务客户端使用 HMMER3 phmmer 进行序列相似性搜索 使用 Perl 客户端和 Docker 的 REST 网络服务 支持协议 3:安装 Docker 并运行 EMBL-EBI 客户端容器 基本协议 5:使用 InterProScan 5 进行蛋白质功能分析 使用 Python 客户端和 Docker 的 REST 网络服务 备用协议 4:使用 InterProScan 5 进行蛋白质功能分析使用 InterProScan 5 RESTful 网络服务与 Java 客户端进行蛋白质功能分析 支持协议 4:安装 Java 网络服务客户端 基本协议 6:通过网络接口使用 Clustal Omega 进行多序列比对 替代协议 5:使用 Clustal Omega 与 Perl 客户端和 Docker 进行多序列比对 支持协议 5:使用 OpenAPI 用户界面探索 RESTful API。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Using EMBL-EBI Services via Web Interface and Programmatically via Web Services

Using EMBL-EBI Services via Web Interface and Programmatically via Web Services

The European Bioinformatics Institute (EMBL-EBI)’s Job Dispatcher framework provides access to a wide range of core databases and analysis tools that are of key importance in bioinformatics. As well as providing web interfaces to these resources, web services are available using REST and SOAP protocols that enable programmatic access and allow their integration into other applications and analytical workflows and pipelines. This article describes the various options available to researchers and bioinformaticians who would like to use our resources via the web interface employing RESTful web services clients provided in Perl, Python, and Java or who would like to use Docker containers to integrate the resources into analysis pipelines and workflows. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC.

Basic Protocol 1: Retrieving data from EMBL-EBI using Dbfetch via the web interface

Alternate Protocol 1: Retrieving data from EMBL-EBI using WSDbfetch via the REST interface

Alternate Protocol 2: Retrieving data from EMBL-EBI using Dbfetch via RESTful web services with Python client

Support Protocol 1: Installing Python REST web services clients

Basic Protocol 2: Sequence similarity search using FASTA search via the web interface

Alternate Protocol 3: Sequence similarity search using FASTA via RESTful web services with Perl client

Support Protocol 2: Installing Perl REST web services clients

Basic Protocol 3: Sequence similarity search using NCBI BLAST+ RESTful web services with Python client

Basic Protocol 4: Sequence similarity search using HMMER3 phmmer REST web services with Perl client and Docker

Support Protocol 3: Installing Docker and running the EMBL-EBI client container

Basic Protocol 5: Protein functional analysis using InterProScan 5 RESTful web services with the Python client and Docker

Alternate Protocol 4: Protein functional analysis using InterProScan 5 RESTful web services with the Java client

Support Protocol 4: Installing Java web services clients

Basic Protocol 6: Multiple sequence alignment using Clustal Omega via web interface

Alternate Protocol 5: Multiple sequence alignment using Clustal Omega with Perl client and Docker

Support Protocol 5: Exploring the RESTful API with OpenAPI User Inferface

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