How To Perform An Advanced Search

The ENA Advanced Search interface interface is a powerful way to search the archive for datasets which meet criteria of interest to you as a user. The below guide will walk you through the interface using examples. Use this to familiarise yourself with the interface before conducting your own searches.

Example Uses

Below are two example cases you can follow to better understand the advanced search interface:

• Find Neanderthal Read Data
• Find Samples Based On Checklists

Find Neanderthal Read Data

Locate all read data submitted for Neanderthals

1. Navigate to the advanced search browser: https://www.ebi.ac.uk/ena/browser/advanced-search

2. The interface first asks you to select the datatype you want to search for. Use the ‘?’ icon next to the drop-down box to learn more about the options. We are searching for read data, so select ‘Raw Reads’:
3. Click ‘Next’

4. You now have opportunity to apply filters which will limit the set of reads which are provided
5. Use the blue buttons on the left to select different filter categories, or use the ‘Type to filter query params’ box to search for a specific parameter
6. In the above box, we have selected the ‘Taxonomy and related’ category, and chosen ‘NCBI Taxonomy’ from the dropdown
7. All submissions to ENA must use a valid species-level taxon from the NCBI taxonomy database. Begin typing and suggestions appear. We have put ‘Neanderthal’. Notice multiple suggestions are given; in this case, they are synonyms, as indicated by their matching taxon IDs (63221)
8. We have entered all the parameters we want, so click ‘Next’ twice to get to the Fields selection box

9. Now click the ‘Manually select fields’ box.
10. For reads, there are three pre-defined field sets you can use: FASTQ Files gives you the archive-generated standardised FASTQ format, SRA Files gives file versions suitable for use with NCBI’s SRA Toolkit, while Submitted Files gives you copies of the files originally submitted by the user
11. You can use the ‘Available Fields’ box to choose any fields you wish to see included in the table of results. Not all of these will always be relevant. For this serach, we have selected the FASTQ Files preset, but if you skip this step you will still be shown a list of accessions with descriptions, by default
12. When you are satisfied with the fields you have chosen, click ‘Search’ to see the results of your query

Find Samples Based On Checklists

ENA sample objects represented physical samples used in sequencing experiments. Users must conform to a checklist of values when submitting samples. We can leverage this in searches to find samples belonging to a checklist which describes materials of interest to us.

Follow the below guide to find samples registered using the checklist named ‘GSC MIxS human gut’, which describes human gut microbiome samples

1. Navigate to the advanced search browser: https://www.ebi.ac.uk/ena/browser/advanced-search

2. The interface first asks you to select the datatype you want to search for. Use the ‘?’ icon next to the drop-down box to learn more about the options. Select the option simply named ‘Samples’
3. Click ‘Next’

4. Categories of search parameters are found by clicking the blue boxes to the left of the page. Select the ‘Database record’ category now
5. In the beige box, use the dropdown box to select the ‘Checklist’ option
6. A new dropdown box will appear: use this to select the checklist you are interested in - ‘GSC MIxS human gut’ in this case
7. Notice the accession number of the checklist, ‘ERC000015’, is added to the ‘Query’ box
8. Now click ‘Next’ twice to get to the Fields selection box
9. You can use the ‘Available Fields’ box to choose any fields you wish to see included in the table of results. Not all of these will always be relevant
10. When you are satisfied with the fields you have chosen, click ‘Search’ to see the results of your query

Rulespace

Rulespace is a tool which allows you save your searches, give them names, rerun them and share them with other people. Learn more about it in the Rulespace Guide.