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NCATSTranslator / Feedback

A repo for tracking gaps in Translator data and finding ways to fill them.
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another incorrect acronym driving results - ASM #479

Open gglusman opened 1 year ago

gglusman commented 1 year ago

https://ui.ci.transltr.io/results?l=Aggressive%20Systemic%20Mastocytosis&i=MONDO:0020333&t=0&q=c0e8f2ed-8e10-4711-bd5f-fed713672e02

Four results, including the sixth strongest score (99.1) follow this pattern:

image

Looking at the supporting papers (linking SMPD1 to the disease), it turns out that Acid Sphingomyelinase is the ASM being misinterpreted as Aggressive Systemic Mastocytosis.

Likewise, a number of results including or relying on 'ibuprofen' derive the evidence from a paper in which ASM means "artificial sputum medium".

Then, the botox (botulinum toxin) result relies on ASM meaning "accessory soleus muscle".

For the dinoprostone, calcitriol and ergocalciferol results, ASM means "airway smooth muscle".

gglusman commented 1 year ago

Retesting CI / 8/17, one of three score-100 results is Melphalan, also linking to Acid Sphingomyelinase (ASM).

gglusman commented 10 months ago

"ASM" still mixes things. Re-test on 2024/1/11: answer Benzbromarone, supporting papers PMC8245819 and PMC4543527, where ASM means 'airway smooth muscle'. Other answers similarly affected. Answer Fluoxetine, supporting paper PMC8198802, ASM = 'acid sphingomyelinase'.

sstemann commented 3 weeks ago

It looks like this is still happening. I'm not sure if it's still a TMKP issue though since this one is from DisGeNet via BTE

https://ui.test.transltr.io/results?l=Aggressive%20Systemic%20Mastocytosis&i=MONDO:0020333&t=0&r=0&q=239eba93-dd62-4311-a085-d567db4bdd7b

image

image https://pubmed.ncbi.nlm.nih.gov/25898364/ https://pubmed.ncbi.nlm.nih.gov/27868341/

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image

andrewsu commented 2 weeks ago

I created an issue (https://github.com/biothings/biothings_explorer/issues/900) to filter out low-scoring edges from disgenet.