Introduction to mining public databases on the Web and with Cytoscape

Date: 26 March 2021

Time: 10:00AM CET

Location: ONLINE! (Zoom)

Requirements: Working knowledge of Cytoscape (CBNA L1P1), computer with Cytoscape installed

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
• Mine Ensembl BioMart for node annotations
• Understand the various annotation systems and their (in)compatibility e.g. Ensembl, RefSeq, Entrez etc.
• Access and use the Network Data Exchange

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 course requires a basic level of understanding of Cytoscape (importing data, manipulating networks, visualisations, AppManager).
You will need your own computer with Cytoscape installed.

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

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

For all NON-EMBL applicants – registration to this course is only possible with your University/Institute official email address. All email registrations with e.g. yahoo, gmail etc will be filtered out. Spaces are limited.

Bookings