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Data Search and Retrieval

Data Search and Retrieval. European Nucleotide Archive. 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)

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Data Search and Retrieval

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  1. Data Search and Retrieval European Nucleotide Archive Nicole Silvester www.ebi.ac.uk/ena

  2. Objectives • Understand the different types of data available from ENA • Know how to find/download them

  3. Data available from ENA • Metadata (XML or tab-separated text) • Flat files • Sequences (FASTA) • Raw reads (FASTQ or submitted format) • Analysis (submitted format)

  4. Searching for data • By accession • By taxon • By search conditions: • Text search • Advanced search • By sequence: • Sequence search

  5. 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

  6. 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&portal=sequence_release&offset=1&length=1000&display=fasta&download=fasta

  7. 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 chosenENA data domain

  8. Text Search vs Advanced Search • want: human sequences

  9. Text Search vs Advanced Search • want: human mRNA sequences

  10. Sequence Search • http://www.ebi.ac.uk/ena/search/

  11. 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

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