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

Area of Science:

• Bioinformatics
• Computational Biology
• Data Science

Background:

• The European Bioinformatics Institute (EMBL-EBI) provides critical bioinformatics databases and analysis tools.
• Programmatic access to these resources is essential for integrating them into analytical workflows and pipelines.
• Web services (REST and SOAP) and containerization (Docker) offer flexible integration options.

Purpose of the Study:

• To describe the methods and options for accessing EMBL-EBI resources programmatically.
• To guide researchers and bioinformaticians in utilizing web services and Docker containers for bioinformatics analyses.
• To facilitate the integration of EMBL-EBI tools into custom analytical pipelines.

Main Methods:

• Utilizing RESTful web services clients in Perl, Python, and Java for data retrieval and analysis.
• Employing Docker containers for seamless integration of EMBL-EBI resources into analysis workflows.
• Demonstrating specific protocols for data retrieval (Dbfetch), sequence similarity search (FASTA, BLAST+, HMMER3), protein functional analysis (InterProScan 5), and multiple sequence alignment (Clustal Omega).

Main Results:

• Successful programmatic access to EMBL-EBI resources is demonstrated through various clients and protocols.
• Integration of core bioinformatics tools into analysis pipelines is achievable using provided methods.
• The article serves as a practical guide with detailed protocols for diverse bioinformatics tasks.

Conclusions:

• EMBL-EBI resources are readily accessible and integrable into computational workflows via web services and Docker.
• Researchers can leverage these tools to enhance their bioinformatics analyses and data processing capabilities.
• The described methods empower bioinformaticians to build robust and reproducible analysis pipelines.