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A Virtual Machine Platform for Non-Computer Professionals for Using Deep Learning to Classify Biological Sequences of Metagenomic Data

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PyCellBase, an efficient python package for easy retrieval of biological data from heterogeneous sources.

Daniel Perez-Gil¹, Francisco J Lopez¹, Joaquin Dopazo^2,3

¹Genomics England, London, UK.

BMC Bioinformatics

|March 30, 2019

Summary

This summary is machine-generated.

PyCellBase offers a Python package for easy access to integrated biological data via the CellBase API. This tool simplifies complex bioinformatic tasks like variant annotation without local database setup.

Keywords:

Annotation CellBase Database Python RESTful Repository Variant

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Area of Science:

Bioinformatics
Computational Biology
Data Integration

Background:

Biological databases are rapidly expanding in diversity and complexity.
Data accessibility and integration pose significant challenges.
CellBase was developed as an integrative solution, centralizing heterogeneous biological data in a NoSQL database.

Purpose of the Study:

To present PyCellBase, a Python package for programmatic access to the CellBase RESTful API.
To provide a user-friendly interface for accessing biological information.
To offer command-line tools for common bioinformatics tasks.

Main Methods:

Developed PyCellBase as a Python package.
Utilized CellBase's RESTful web service API.
Integrated command-line tools for bioinformatic tasks.

Main Results:

PyCellBase enables fast and user-friendly access to biological data.
No local database installation is required.
Variant annotation and other bioinformatic tasks are facilitated.
CellBase ensures high availability and real-time query performance.

Conclusions:

PyCellBase provides efficient access to heterogeneous biological information.
Facilitates tasks like variant annotation requiring comprehensive knowledge resources.
Enables integration of results into Python applications and pipelines.