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Ignore genes in GO-CAM JSON files that aren't used in the model #1262

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kimrutherford opened this issue Feb 27, 2025 · 0 comments
Open

Ignore genes in GO-CAM JSON files that aren't used in the model #1262

kimrutherford opened this issue Feb 27, 2025 · 0 comments
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kimrutherford commented Feb 27, 2025 •
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As an example, we should ignore SPAPB2B4.06 when loading the GO-CAM JSON for 678073a900002931 because it's not used in the model:
https://www.pombase.org/gocam/gene/678073a900002931/SPAPB2B4.06

The fix is to filter genes (and modified proteins / complexes?) that don't enable an activity.

Another example is SPAC4D7.04c / rer2 which isn't in the model for 665912ed00000459

See also:

Edit:

For checking after the fix, here are the unused genes in all pombe models:

model_id gene_id gene_name
66187e4700001781 SPBC428.08c clr4
663d668500002178 SPAC607.04 arg82
665912ed00000459 SPAC4D7.04c rer2
665912ed00000459 SPAC7D4.09c dfg10
665912ed00000652 SPBC428.08c clr4
665912ed00001983 SPBC428.08c clr4
6690711d00000916 SPAC4G9.10 arg3
6690711d00002904 SPBC11B10.02c his3
67086be200000251 SPAC4A8.11c fas2
678073a900002636 SPAC4A8.11c fas2
678073a900002931 SPAC4A8.11c fas2
678073a900002931 SPAPB2B4.06 SPAPB2B4.06
678073a900003902 SPBC21C3.08c car2
@kimrutherford kimrutherford self-assigned this Feb 27, 2025
kimrutherford added a commit to pombase/pombase-gocam that referenced this issue Feb 27, 2025
@kimrutherford
Rename RawModel to SerdeModel, make it private
ae7b71f 
Refs pombase/pombase-chado#1262
kimrutherford added a commit to pombase/pombase-gocam that referenced this issue Feb 27, 2025
@kimrutherford
Rename GoCamModel to GoCamRawModel
c2b78e4 
We'll use "GoCamModel" for the higher level model.

Refs pombase/pombase-chado#1262
kimrutherford added a commit to pombase/pombase-gocam-process that referenced this issue Feb 27, 2025
@kimrutherford
Add get_connected_genes(), find_detached_genes()
110421a 
Also rename GoCamModel to GoCamRawModel.  We'll use "GoCamModel" for
the higher level model.

Refs pombase/pombase-chado#1262
kimrutherford added a commit to pombase/pombase-gocam-process that referenced this issue Mar 1, 2025
@kimrutherford
Return the ID from find_detached_genes()
f88c56e 
Refs pombase/pombase-chado#1262
kimrutherford added a commit to pombase/pombase-gocam-process that referenced this issue Mar 1, 2025
@kimrutherford
In find_detached_genes(), ignore annotated genes
9b14202 
Some genes don't "enable" an activity but they are annotated we a
component or process.

Refs pombase/pombase-chado#1262
kimrutherford added a commit to pombase/pombase-gocam-tool that referenced this issue Mar 1, 2025
@kimrutherford
Add detached-genes sub-command
a511d98 
Refs pombase/pombase-chado#1262
kimrutherford added a commit to pombase/pombase-gocam-process that referenced this issue Mar 1, 2025
@kimrutherford
Fix get_connected_genes() to avoid duplicates
1b9e45b 
Refs pombase/pombase-chado#1262
kimrutherford added a commit to pombase/pombase-gocam-process that referenced this issue Mar 2, 2025
@kimrutherford
Handle "bare" genes as input or output
d267928 
Refs pombase/pombase-chado#1262
kimrutherford added a commit to pombase/pombase-gocam-process that referenced this issue Mar 2, 2025
@kimrutherford
Remove next/previous nodes fields from node struct
b57a916 
We'll implement next/previous as methods on the model.

Refs pombase/pombase-chado#1262
kimrutherford added a commit to pombase/pombase-gocam-process that referenced this issue Mar 3, 2025
@kimrutherford
Refactor to use GoCamModel in more places
7109506 
Instead of GoCamRawModel directly.

Refs pombase/pombase-chado#1262
kimrutherford added a commit to pombase/pombase-gocam-tool that referenced this issue Mar 3, 2025
@kimrutherford
Update pombase-gocam-process version
f57e6fe 
Refs pombase/pombase-chado#1262
kimrutherford added a commit to pombase/pombase-gocam-tool that referenced this issue Mar 3, 2025
@kimrutherford
Refactor to use GoCamModel in more places
1213425 
Instead of using GoCamRawModel directly.

Refs pombase/pombase-chado#1262
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