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Sage-Bionetworks / schematic

Package for biomedical data model and metadata ingress management
https://schematicpy.readthedocs.io/en/latest/cli_reference.html
MIT License
21 stars 24 forks source link

Add a suggested replacement in validation #1258

Open allaway opened 12 months ago

allaway commented 12 months ago

Is your feature request related to a problem? Please describe. Sometimes, our investigators submit a slightly wrong version of a correct term. Eg. the correct term for a particular mouse model could be Nf1flox/flox, but they will submit Nf1-Flox/Flox.

Describe the solution you'd like It would be helpful for the app/validation to suggest the closest match from the schema - e.g. "Did you mean Nf1flox/flox?" It would be EVEN BETTER! :) if the user could then just click yes to incorporate that change, rather than having to change the csv by hand.

How important is this feature? Select from the options below: • 🏝 Low - it's an enhancement but not crucial for work

When will use cases depending on this become relevant? Select from the options below: • Short-term - 2-4 weeks

Additional context Here's a guide to comparing text with different techniques and metrics: https://mariogarcia.github.io/blog/2021/04/nlp_text_similarity.html

allaway commented 12 months ago

Related to this, the current error message is not super helpful with large sets of valid terms:

e.g.:

'Nf1-Flox/Flox' is not one of ['hTERT NF1 ipNF95.11b C/T', 'JHU 2-103-PDX', 'cNF97.2a', 'GM23338', 'cNF04.9a', 'B6.129S2-Nf1tm1Tyj/J', 'sNF96.2', 'WT ES', 'M3 MPNST', 'sNF02.2', 'C57BL/6J', 'hTERT NF1 sipnNF95.12B', 'HEK293 NF1 -/- with R681X mNf1 cDNA', '3PNF_SiPSsv_MM_11', 'GM11602', 'GFAP-Cre; Nf1-G848R/Flox', 'HEK293 NF1 -/- clone 2', 'hTERT SC ipn97.4', 'Schwann cell NF1 -/- with R816X mNf1 cDNA', 'HEK293 NF1 -/- with WT tagged mNf1 cDNA', 'Nf1-/- HEK 293', 'iPSC NF1 +/- BJFF.6 bkgd', 'iPSC

AmyHeiser commented 11 months ago

Thanks for the feature request @allaway We are now pointing users to our Jira Service desk for requests. So I will move this one, but wanted to let you know since we don't monitor this any longer.

allaway commented 11 months ago

Thanks Amy! Maybe to prevent others from having issues get lost (or prevent me from making new ones here when I inevitably forget.... 😄 ), we could delete the issue templates from this repository and replace with a template that directs users to the service desk? What do you think? I am happy to make a pull request for this.

AmyHeiser commented 11 months ago

Thanks Robert!