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Attach timestamps to genes #1164

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dondi opened this issue Jan 22, 2025 · 2 comments
Open

Attach timestamps to genes #1164

dondi opened this issue Jan 22, 2025 · 2 comments
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@ceciliazaragoza @ntran18
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code review database priority 0.5

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@dondi
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dondi commented Jan 22, 2025

Emerging from the discussion of #1120, we have resolved that the gene table should itself have a timestamp. Even if a high percentage of genes will be the same from year to year, producing nearly the same records, we also don’t want to include genes that didn’t exist at a particular time with the interactions from that time
@ntran18 ntran18 self-assigned this Feb 9, 2025
ntran18 added a commit that referenced this issue Feb 9, 2025
@ntran18
#1164 #1165 Fixing the schema for gene regulatory network and protein…
8f856be 
… protein interactions to have timestamp and for gene and protein tables and annotation type for physical interactions table
@dondi
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dondi commented Feb 26, 2025

@ceciliazaragoza reported that initial queries that include the timestamp now run without errors, but for ZAP1, which regulates itself, the updated query does not return the expected self-regulation adjacency item

@kdahlquist checked the 2025 data and confirmed that ZAP1 does still regulate itself, so @ceciliazaragoza will investigate the query further. @ntran18 can investigate the latest loaded data to see if the issue resides in the database scripts instead

@ntran18
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ntran18 commented Feb 26, 2025

The issue with ZAP1 is not from the database queries but from the scripts that getting data from AllianceMine. I checked the script, and we don't get data that have ZAP1 self-regulated. I have to investigate the queries more.

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