- To learn how to navigate the EBI website and the different ways to access and retrieve data.
- Exposure to the depth and variety of tools and databases available at the EBI.
- A brief overview of the major databases at EBI.
- To understand the differences between the major nucleotide sequence databases.
- To browse the ENA database in detail, learning about its structure and the type of data it contains.
- To learn the different ways to access sequence data (DBFetch, ENA browser...).
ENA (European Nucleotide Archive)
Protein Sequence Databases
- To understand the differences between the major protein sequence databases.
- To browse the UniProt database in detail, learning about its structure and the type of data it contains.
- To learn the different ways to access sequence data (sequence search, text search...).
UniProt
Sequence Searching and Alignment
- To understand the principles of nucleotide and protein sequence searching.
- To learn about the different sequence searching tools available at the EBI (including Blast, Fasta and iterative searches), and which ones are appropriate for different applications.
- To gain familiarity with the different sequence alignment tools available.
- To understand the specialised sequence search tools within the InterPro database and how they are used to predict protein classification and function.
- To browse the InterPro database, learning about the type of annotation it contains.
InterPro
Interactions & Pathways
- To understand what is to be found in a molecular interaction database, alternative data formats and the various tools designed to work with them.
- To learn how to explore reactions and pathways
- To gain familiarity with specialised tools, such as analysis of expression data.
IntAct
Reactome
ArrayExpress: Public database for transcriptomics data & Gene Expression Atlas
- How to browse and retrieve data from the ArrayExpress public repository of transcriptomics data. Data formats for transcriptomics data and submission to ArrayExpress can be covered in a separate lecture.
- How to browse and retrieve data from the Gene Expression
- How to query for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples correlations
ArrayExpress
Atlas
Gene Expression Data analysis
This LECTURE covers the basics of gene expression data analysis introducing the fundamental statistical concepts and methodologies used to analyze this data.
Ensembl for new Ensembl users
- To learn about genome annotation with a focus on vertebrates and other eukaryotes;
- Practical experience in data mining approaches based on BioMart;
- How to look at comparative genomics data (gene trees and homologies) and sequence variation (including structural variation).
Ensembl
Standards and Ontologies
- Introduction to the Gene Ontology; the structure and concepts
- Annotation to the Gene Ontology; including how to access GO annotations
- Practical uses of GO for researchers; including GO slims and an overview of some term enrichment tools
GO
GOslims
Small Molecule and Enzyme Resources in Bioinformatics
- To learn how to search for small molecules and understand their chemical ontology and associated bioactivity data.
- To learn about structure representation and search algorithms.
- Understand how to extract bioactivity data to construct potential structure-activity relationships
ChEMBL
ChEBI
IntEnz
Rhea
Full Day Training Modules
Module Title
Contents/Learning Objectives
Resources and Tools
Mass Spectrometry based Proteomics
- How to browse and retrieve data from the PRIDE public repository of proteomics data.
- To gain practical experience in querying the database and extracting information about identifications of proteins, peptides and protein modifications.
- To introduce three PRIDE auxiliary projects: OLS (ontology lookup service), PICR (Protein Identifier CrossReference service) and DoD (Database On Demand).
PRIDE
BioMart
PRIDE Converter
OLS/PICR
Ensembl
for more advanced Ensembl users
- To learn about genome annotation with a focus on vertebrates and other eukaryotes;
- Practical experience in data mining approaches based on BioMart;
- How to look at comparative genomics data (gene trees and homologies) and sequence variation across populations;
- A deeper look into comparative genomics, sequence variation (including structural variation), and gene regulation
Ensembl
Ensembl genomes
for more advanced Ensembl users
- To learn about genome annotation with a focus on bacteria, protists, fungi, plants and invertebrate metazoan;
- Practical experience in data mining approaches based on BioMart ;
- How to look at comparative genomics data (gene trees and homologies) and sequence variation across populations;
- A deeper look into comparative genomics, sequence variation (including structural variation), and gene regulation
Ensembl genomes
Structures
- To understand the fundamentals of protein structures tertiary and quaternary structures and structure quality.
- To learn how to search, retrieve, visualise and analyse structures and their bound inhibitor, or drug molecule environments.
- To analyse similar structures, small structural motifs and similar interfaces.
PDBe
Small Molecules in Bioinformatics
- To learn how to search for small molecules and understand their chemical ontology and associated bioactivity data.
- To learn about structure representation and search algorithms.
- Understand how to extract bioactivity data to construct potential structure activity relationships .
