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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.

@dondi dondi mentioned this issue Mar 11, 2025
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ntran18 added a commit that referenced this issue Mar 12, 2025
@ntran18
#1120 #1164 Change the database schema to make sure gene or protein w…
63baa11 
…ith different timestamps can be added to the database when adding same data with different timestamps
ntran18 added a commit that referenced this issue Mar 12, 2025
@ntran18
#1120 #1164 Remove all files and code related to filtering or updatin…
e939f93 
…g data to the database
dondi added a commit that referenced this issue Mar 12, 2025
@dondi
Merge pull request #1185 from dondi/maika-database
afc1936 
#1120 #1164 Fix for updating data
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