Context search panel
Last updated
Last updated
This feature is experimental, and only available to users in some initiatives (e.g. PATH-SAFE)
The Context Search panel is for finding genomes that are contextually linked to a selected group of genomes in the current Collection. This functionality allows you to contextualise your genomes using other uploaded genomes (you can select which folders, countries, dates, and allele distance threshold to include in the context search).
The context search brings in genomes that were not part of your initial collection, but which are similar enough to those initial genomes to be worthy of further investigation. If they are from another data owner, you will be able to ask your colleagues at that agency for more information, and you can together determine if there’s additional metadata that would be valuable for further investigation.
To add context genomes, Click the "Open Context Search" button in the menu on the Interactive Collection View, and choose the you want to apply to the search.
The Threshold allows you to change the sensitivity of the allelic distance between the Search’s genomes and the genomes that meet your other search criteria.
The “Folders” section allows you to select from all public Folders, as well as any Folders you can access with your login account. Genomes in selected Folders will be searched for relevance.
The "Countries" section allows geographic filtering in case you only want to pull genomes from specific areas into your context search. This search relies on metadata columns.
“Time” section allows you to pull genomes from specific timeframes into your context search. The Time filter uses the year/month sample date (i.e. this is the date the sample was collected/received, not the date the genome was submitted to the PATH-SAFE platform).
Once the search has been completed successfully, click the Create Collection button to create a new collection with the resulting context genomes added.
Note that a new tree will not be generated automatically. You will need to generate a new tree in the new Collection.
