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Finding similar accessions

Similarity Search helps you explore potential duplicate accessions on Genesys.

The Similarity Search function is available to registered users only. Create an account if you want access.

Why similarity search matters​

A curator will be interested to know whether they hold multiple samples of the same material, and a network whether it holds the same material in multiple genebanks. Users might be interested in alternatives to an accession that is not available.

DOIs can reliably and unambiguously identify a specific sample, which helps with this sort of analysis. The GLIS DOI Portal scans the internet for connections between DOI-enabled PGRFA and can link accessions held in different genebanks. However, DOI adoption for PGRFA remains optional, so only a subset of conserved crop diversity can be linked in this way using fully automated tools. Even accessions that do have a DOI often do not link back to the material from which they were sourced, because those DOIs were not known at the time of acquisition.

Absent DOIs, it is therefore necessary to compare all the available passport data of two accessions and make a determination as to how likely they are to be genetic duplicates.

Once registered, you can start a similarity search from the accession details page by clicking the Similar button at the top right.

Finding similar accessions from the accession details page

Understanding the results​

Genesys compares the selected accession with the entire database of 4.5 million records and returns a limited number of potential matches, with the best matches first. The candidate match is displayed side-by-side with the selected accession so you can evaluate the results, and decide what to do.

Side-by-side comparison of the selected accession and a candidate match

The results bar shows the currently selected match in the middle, with buttons to navigate to the next and previous matches to the right and left, respectively.

Navigation bar for browsing through similar accession candidates

Recording your results​

It helps to record the results of the similarity search, so you do not need to re-evaluate the same pair of accessions again in the future.

How does Genesys do it?​

To find accessions with similar passport data to your selected accession, Genesys uses the following approach:

  1. Standardized values: All the passport data fields of candidate accessions are compared using their standardized or coded values.

  2. Free-text matching: For free-text fields like description of collecting site, a combination of both the Sørensen-Dice coefficient and the Levenshtein distance is used.

  3. Alias matching: The scores arising from the field-by-field comparisons are added to the score of each unique name and other number (aliases) of the accession.

  4. Similarity rating: After scoring all candidates, the 20 highest scoring matching candidates are given a similarity rating.

  5. Score capping: When the score of the best candidate is very high, all other good candidates end up with a low ranking. To help ensure good candidates remain visible, Genesys caps the maximum advantage of the top-ranked candidate at approximately 80%.