CBNA 2021 L1P2: Introduction to mining public databases in Cytoscape (BioMart, String, IntAct)

Matt Rogon   2021-03-26   Comments Off on CBNA 2021 L1P2: Introduction to mining public databases in Cytoscape (BioMart, String, IntAct)

Date(s) - 2021-03-26
10:00 CET - 17:00 CET



Introduction to mining public databases in Cytoscape (BioMart, String, and others)

Date: 26 March 2021
Time: 10:00 – 17:00
Location: ONLINE! (Zoom)
Requirements: Working knowledge of Cytoscape (CBNA L1P1), computer with Cytoscape installed

Course L1P2 – Level 1, Part 2

Cytoscape is a multi-platform open-source tool for visualising interaction networks and integrating them with annotations, multi-omic profiles and other state data.
Cytoscape allows us not only to create networks out of our own pre-formatted data files, but also to download such networks from public databases, and annotate them with public data such as cross-mapping among various identifiers (ensembl, refseq, uniprot etc), gene/transcript/protein annotations (including descriptions, chromosomal locations), homologies, ontologies, domains, and many many more.

Course goals:

During this 1 day course you will learn how to:

  • access an array of databases containing interactions (String, IntAct, and others)
  • build networks from those databases,
  • integrate multiple databases together
  • as well as add annotations and knowledge from the public repository at ENSEMBL (BioMart)

After the course you will be able to access public repositories of networks and attributes to mine massive amounts of knowledge onto your own networks.

This is a Level 1 introductory course, working knowledge of Cytoscape is required – see CBNA Course L1P1. You will need your own computer with Cytoscape installed (exact details will follow in an email closer to the course).

If you would like to register to receive these announcements early, please send an empty message with the title ‘Subscribe’ to

If you have further questions please don’t hesitate to contact us.

Please note that this and all the other courses are pending recommendations from the Director General regarding current COVID-19 situation.

Best wishes,

Upcoming courses in the series:

Course 3 – (4-days) Ontologies course in collaboration with SCB Gibson Team, and deNBI.

Course 4 – (2-half-days) Mining Biomedical Data – Part 2 – Accessing public databases for data retrieval pathways (KEGG, Reactome, NDex), drugs, and *diseases.


Attend the course from any EMBL outstation without physically attending in Heidelberg