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monarch-initiative / monarch-app

Monarch Initiative website and API
https://monarchinitiative.org/
BSD 3-Clause "New" or "Revised" License
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Feedback form - Tim Putman - /overview page is out of date and now very inaccurate. Al... #436

Closed monarch-issues-tracker[bot] closed 1 year ago

monarch-issues-tracker[bot] commented 1 year ago

Name Tim Putman

Email timeput@gmail.com

GitHub Username @putmantime

Details Page: /overview Browser: Chrome 118.0.0.0 Device: Apple Macintosh OS: Mac OS 10.15.7 Engine: Blink 118.0.0.0

/overview page is out of date and now very inaccurate.

All of this is out of date and describes the old stack. We need to bring it down and replace it with content about our new stack.

vincerubinetti commented 1 year ago

Maybe one of the paper figures could go there? Otherwise, should immediately replace it with a "coming soon" block.

sagehrke commented 1 year ago

Comment from @monicacecilia

The information on the Overview page has aged and is outdated. Need to include:

updated figure outlining infrastructure updated text describing how it works (can come from the NAR paper) updated links to pertinent repos (kg building, ingest, etc.)

monicacecilia commented 1 year ago

Use this Sankey figure to update the content.

Legend:

Data harmonization within the Monarch KG. The three primary data types in the Monarch KG are genes, diseases, and phenotypes (A). This image details their entity (node) and link (edge) counts and the unifying ontologies (D) by which the source data (B) and ontologies (C) are harmonized. Cross-species inference (E) is accomplished via gene orthology, homology, and phenotype similarity. Content dissemination (F) is via API, the Monarch UI, and within the clinical application Exomiser. Note that the figure expresses only a portion of the integrated ontologies (column C). For a comprehensive list see PHENIO documentation (linked below). In Column D, GO: Gene Ontology; BP: Biological Process; MF: Molecular Function; CC: Cellular Component.

Figure 3 Monarch NAR-02806-Data-E-2023.pdf

Other links below should be updated/removed as appropriate.

glass-ships commented 1 year ago

I've updated the overview page in #463 - you can see the preview here

Let me know if there's any updates/edits you'd like to see