Comments (2)
Agreed. I have reworked the gene search typeahead functionality in release 4.11. This new behavior will try to match on the gene symbol first. If there are no matches, it will search the gene aliases. In your example, the current behavior results in this long list of 'hits':
In gene.iobio 4.11, the search on F5 will return only that gene:
Here is a more complicated example. If we type in 'MA', we get a long list of genes starting with 'MA'. Type in 'MAY' and we only get one hit, and it is for the gene alias 'MAYA'. In other words, not gene names starting with 'MAY' were found in the database based on the names populated from RefSeq and Gencode, but there is an alias starting with 'MAY' that points to the GenCode gene MNX1-AS1.
![Screenshot 2024-06-17 at 5 24 06 PM](https://private-user-images.githubusercontent.com/8420103/340483618-c51a32ca-fa3a-412e-9c46-de3c18e03233.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.hItlotlLQFO-mtcVxUwN2dKXSqDFSCFs9lZfRiLET_U)
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@AlistairNWard, you bring up an interesting point about the order of the gene names returned. In the new release, the search looks for a match based on the beginning of the gene name. Hopefully, this isn't too restrictive. If we returned all genes that match the term anywhere in the gene name, then the order of the genes returned is more relevant. And I agree with you. The user would want to see the 'closest' matches first. And the new behavior does satisfy this. For example, if the user searches on gene TAT, that exact match appears first in the list:
And on a related note, gene list order is dictated by the gene name, not the gene alias. So, for example, if the user enters MGC445, there are not any genes with this name, but there are gene aliases that start with this term. Notice that the genes are ordered alphabetically by the gene name (the name designated by RefSeq or Gencode).
There are many nuances to the gene search, so please feel free @AlistairNWard to play around with the new functionality on https://stage.gene.iobio.io. Overall, I'm happy with the new behavior, but my guess is that it may still need some refinement. Hopefully, this gets us closer to a solid gene search.
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Related Issues (20)
- Bypassing unknown genes stops analysis? HOT 1
- When gene is launched from Mosaic, warn user when required files not present
- Handle new Mosaic variant annotation field name with version (e.g. fieldName_XXXXX@version)
- When gene added from gene search, don't go to variant's tab unless a variant for the added gene is added HOT 1
- Annotate variants with SpliceAI, CADD, Mutscore, Alphamissense, Eve
- Send file paths to Anders
- Test with gnomAD and ClinVar annotations (edit TOML)
- Reference is not being handled correctly HOT 20
- globalApp as global mixin does not contain latest state
- Get rid of getClinvarVariantsV2, freebayesJointCallV2, and annotateVariantsV2 (and getClinvarVariants, freebayesJointCall, and annotateVariants.
- Clean up code that initializes iobio backend.
- When an alias is substituted for a gene w/o transripts, make sure the gene coords are the same
- New ClinVar classifications that will split CLINSIG into 3 separate classifications.
- Handle unknown gene gracefully when gene.iobio launched with variant set
- Add validation when gene.iobio is launched from Mosaic, so that the user is given an informative error message. HOT 7
- Display Mosaic project in Nav bar when app launched from Mosaic
- ClinVar GRCh37 links missing variant id in URL
- Adding a note to a variant selected from the variants card fails due to null reference
- When switching between advanced and basic/simple mode, variant interpretation and notes are lost
- Coverage glyphs on gene buttons are not getting refreshed when coverage cutoffs change applied
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