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Data Search and Retrieval

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Presentation on theme: "Data Search and Retrieval"— Presentation transcript:

1 Data Search and Retrieval
European Nucleotide Archive Nicole Silvester

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<ACCESSION>
Retrieve XML format Retrieve Flat file Retrieve FASTA sequence

6 Taxon entry point Retrieve FASTA sequences NCBI tax ID Scientific name
Scientific name Retrieve FASTA sequences uence_release&offset=1&length=1000&display=fasta&download=fasta

7 Text Search vs Advanced 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

8 Text Search vs Advanced Search
want: human sequences

9 Text Search vs Advanced Search
want: human mRNA sequences

10 Sequence Search

11 Resources

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