Recorded webinar

Programmatic access to UniProt using Python

UniProt is a comprehensive, expert-led, publicly available database of protein sequence, function and variation information.

This webinar will give an overview of programmatic access to the UniProt database using Python and cover key aspects of protein entry searches, data filtering, batch downloads and give examples of further processing of downloaded target data.

Following a brief introduction to UniProt services, where to find relevant documentation and help features, the webinar will focus on worked examples. These will include how to programmatically search and retrieve protein entries and sequences, within the results we will then show how to align orthologous sequences and filter for features of interest. 

The webinar will also cover programmatic examples of the UniProt Retrieve/ID mapping service, batch downloads, processing, filtering data by annotation type, and retrieval of recently published proteomics-derived post-translational modification data.

Who is this course for?

This webinar is aimed at life science computational and wet-lab scientists that would find programmatic access to the UniProt database useful. A moderate proficiency in Python is required, however the webinar will cover principles which can be applied to other programming languages. An undergraduate level knowledge of protein biology will be useful.

Outcomes

By the end of the webinar you will be able to:

  • Identify the different routes to access UniProt data and know how to pick the most appropriate for your workflow
  • List the UniProt services such as UniProtKB, Proteomes, UniParc and UniRef
  • Find documentation and useful help to guide your programmatic access
  • Retrieve full UniProtKB entries or specific fields using Python
  • Filter entries by annotation types and other target characteristics

DOI_disc_logo DOI: 10.6019/TOL.UniProtPython-w.2021.00001.1

This webinar took place on 29 September 2022. Please click the 'Watch video' button to view the recording.

This webinar took place previously on 17 November 2021. You can watch a recording of that webinar here and access the slides.

EBI Resources

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Duration: 01:11:40
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29 September 2022
Online
Free
Contact
Anna Swan

Organisers
  • Anna Swan
    EMBL-EBI

Speakers
  • Emily Bowler-Barnett
    EMBL-EBI
  • Aurelien Luciani
    EMBL-EBI

Creative Commons

All materials are free cultural works licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, except where further licensing details are provided.


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