CBNA 2020: Mining Biomedical Data with Networks (BioMart, Ontologies, Complexes, Pathways)

Matt Rogon   2020-04-29   Comments Off on CBNA 2020: Mining Biomedical Data with Networks (BioMart, Ontologies, Complexes, Pathways)

Date(s) - 2020-04-29
10:00 CEST - 17:00 CEST


In 2020 the EMBL Centre for Network Analysis (CBNA) will offer (in collaboration with Bio-IT, de.NBI, and others) a series of courses focusing on data analysis, multi-omic data integration, advanced visualisation, automation, and interpretation using networks and Graph theory.

All of these courses are free and open to EMBL researchers and staff from all sites.

All of these courses will be available online via Zoom regardless of the Coronavirus developments.

Today we open registration for the second course in the entire series:

**CBNA Course Series 2020**: Mining Biomedical Data with Networks (BioMart, Ontologies, Complexes, Pathways)
**Date**: 29 April 2020
**Time**: 10:00 – 17:00
**Location**: ONLINE! (Zoom)
**Requirements**: working (basic) knowledge of Cytoscape, laptops, and enthusiasm

**Course goals:**

    During this 1-day course participants will learn how to access and export data from public resources including:

  • Ensembl BioMart – attaching metadata to bio-molecules e.g. cross-mapping between various annotation systems (Ensembl, RefSeq, UniProt, Entrez etc), annotating chromosomal positions, adding gene descriptions, protein/gene/transcript annotations and many more. (transitioned from the first course – EBI assures it will be back up within a week)
  • Ontologies – these simplest forms of a network (trees) are also the basic form of biological data storage – you will learn how to access Gene, Drug, and Disease ontologies to build maps such as the recent Krogan lab paper for Coronavirus drug repurposing (
  • Pathway databases focusing in detail on KEGG and Reactome.
  • Protein complexes from EBI Complex Portal and Corum database.
  • NDex (network data exchange) system for accessing pathway resources provided by hundreds of labs across the globe.
  • Enrichment Analysis tools in Cytoscape will be used to identify significantly enriched pathways in subnetworks and within lists of molecules

All tools will be introduced through their Web interface as well as via the Cytoscape GUI.
After the course you will be able to independently extract data from public databases, assess their quality, annotate your own networks and biomolecules with them in Cytoscape.

This is a Level 2 introductory course, which requires a (basic) working knowledge of Cytoscape. You will need to have Cytoscape installed on your own computer with a few plugins (details will follow).

This course is available via remote participation, connection details will be provided after registration.

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.
This email may reach you multiple times via different mailing lists.

Best wishes,
Matt Rogon

REQUIRED: Familiarity with Cytoscape (Experience or participation in course level 1)

Upcoming CBNA Courses 2020 (registration opening will be announced):

  • Course 3 (TBA): – Introduction to Network Topology (centralities, shortest path algorithms, clustering, modularity detection)
  • Course 4 (TBA): – Visualisation with Cytoscape and Automation (with a special invited guest: John “Scooter” Morris, UCSF, Cytoscape Core developer)
  • Course 5 (TBA): – Enrichment Analysis with Ontologies and Pathways
  • Course 6 (TBA): – Intermediate Network Analysis and Visualisation (R, iGraph,
  • Course 7 (TBA): – Multi-omic data integration using networks (R, iGraph, Cytoscape)(TBA)



Bookings are closed for this event.