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

Fábio Madeira¹, Nandana Madhusoodanan¹, Joon Lee¹

¹European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

Current Protocols in Bioinformatics

|May 1, 2019

Summary

This summary is machine-generated.

The European Bioinformatics Institute (EMBL-EBI) offers vital bioinformatics databases and tools. Researchers can access these resources programmatically via web services and Docker containers for integrated analysis pipelines.

Keywords:

REST SOAP bioinformatics resources bioinformatics tools programmatic access web services workflows

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

The European Bioinformatics Institute (EMBL-EBI) is a crucial hub for biological data.
Access to EMBL-EBI resources is essential for modern biological research.
Programmatic access facilitates integration into complex analytical workflows.

Purpose of the Study:

To outline the methods for accessing EMBL-EBI resources programmatically.
To detail the use of web services (REST and SOAP) for data retrieval and analysis.
To explain the integration of EMBL-EBI tools into computational pipelines using clients and containers.

Main Methods:

Utilizing RESTful and SOAP web services for programmatic data access.
Employing client libraries in Perl, Python, and Java for resource integration.
Leveraging Docker containers to streamline the incorporation of EMBL-EBI tools into analysis workflows.

Main Results:

Demonstrated availability of diverse bioinformatics databases and analysis tools via web services.
Provided practical guidance on using programmatic access methods for researchers.
Enabled seamless integration of EMBL-EBI resources into custom analytical pipelines.

Conclusions:

EMBL-EBI resources are accessible programmatically, enhancing research capabilities.
Web services and Docker containers offer flexible integration options for bioinformaticians.
These access methods support the development of robust and reproducible biological analyses.