European Nucleotide Archive

Data Search and Retrieval

Nicole Silvester

www.ebi.ac.uk/ena

Objectives

• Understand the different types of data available from ENA

• Know how to find/download them

Data available from ENA

• Metadata (XML or tab-separated text)

• Flat files

• Sequences (FASTA)

• Raw reads (FASTQ or submitted format)

• Analysis (submitted format)

Searching for data

• By accession

• By taxon

• By search conditions:

• Text search

• Advanced search

• By sequence:

• Sequence search

Accession entry point

• http://ebi.ac.uk/ena/data/view/<ACCESSION>• http://www.ebi.ac.uk/ena/data/view/ERS027401

• Retrieve XML format• http://www.ebi.ac.uk/ena/data/view/ERS027401&display=XML

• Retrieve Flat file• http://www.ebi.ac.uk/ena/data/view/AF059042&display=TEXT

• Retrieve FASTA sequence• http://www.ebi.ac.uk/ena/data/view/AF059042&display=FASTA

Taxon entry point

• NCBI tax ID

• http://www.ebi.ac.uk/ena/data/view/Taxon:6643

• Scientific name

• http://www.ebi.ac.uk/ena/data/view/Taxon:Octopus

• Retrieve FASTA sequences• http://www.ebi.ac.uk/ena/data/view/Taxon:6643&subtree=true&p

ortal=sequence_release&offset=1&length=1000&display=fasta&download=fasta

Text Search vs Advanced Search

• Text search:

• “full text” search

• terms searched against data files

• searches across all ENA data domains

• Advanced search:

• “field-based” search

• search against specific meta-data fields

• searches within chosen ENA data domain

Text Search vs Advanced Search

• want: human sequences

Text Search vs Advanced Search

• want: human mRNA sequences

Sequence Search

• http://www.ebi.ac.uk/ena/search/

Resources

• http://www.ebi.ac.uk/ena/about/browser

• http://www.ebi.ac.uk/ena/about/marker-portal-web-interface

• http://www.ebi.ac.uk/ena/about/taxon-portal-web-interface

• http://www.ebi.ac.uk/ena/about/data_download

• http://www.ebi.ac.uk/ena/about/sequence_download

• http://www.ebi.ac.uk/ena/about/read_download

• http://www.ebi.ac.uk/ena/about/sequence_search