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The Monarch Initiative Helpdesk
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Feedback form - Ken Longo - I'm curious how frequently data sources are updated in th... #108

Open monarch-issues-tracker[bot] opened 10 months ago

monarch-issues-tracker[bot] commented 10 months ago

Name Ken Longo

Email longoka@me.com

GitHub Username @longoka

Details Page: /feedback Browser: Chrome 119.0.0.0 Device: Apple Macintosh OS: Mac OS 10.15.7 Engine: Blink 119.0.0.0

I'm curious how frequently data sources are updated in the old or new Monarch sites, including the files (e.g., *.tsv) available in the download area (I assume the data source is identical between both sites)?

As a motivating example, I noticed that for species = "Homo sapiens" the phenotype "BMI-adjusted waist-hip ratio" is not tagged to the gene "INHBE" for the variant "rs150777893-C" from the study "GCST90176019" in the GWAS Catalog (https://www.ebi.ac.uk/gwas/studies/GCST90176019). This study was published 2022-08-23.

Is this an inadvertent omission, a deliberate exclusion based on some filtering criteria, or a backlog issue?

kevinschaper commented 9 months ago

Hi @longoka,

Thanks for submitting these questions, this is important info that we need to make more visible.

The data between versions of the site is actually not the same, and the old site hasn't been updated since 2021. We found ourselves in a tough position and focused all of our effort on bringing up the new site, with new data ingests and a simplified data model that aligns to the biolink model.

The new data will be updated monthly (generally mid-month, so that we include the beginning of the month Mondo release).

longoka commented 9 months ago

Hi @kevinschaper ,

Thank you for that info, and I'm excited to see how the new site develops.

Will the new site offer similar download access to the subject-object tsv files that the old site had? Are updated versions of these files (or some comparable format like json) currently available from one of the github repos?

Thanks