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pombase / pombase-chado

PomBase code for accessing Chado
MIT License
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strange evidence in report for go #418

Closed pombase-admin closed 9 years ago

pombase-admin commented 9 years ago

http://curation.pombase.org/dumps/latest_build/logs/log.2015-01-23-04-40-03.gaf-load-output

has

reading go_proc.txt no taxon filter - annotation will be loaded for all taxa

5605 | Microscopy 6 | immunofluorescence evidence 15 | RNA protection assay evidence

but we don't use these evidences for GO?

(also function)

Original comment by: ValWood

pombase-admin commented 9 years ago

Actually, I remember now, I think htis is culmulative, BUT the totals are the same every time. it seems to have changed so that now it is just showing the Phenotype totals maybe???

Original comment by: ValWood

pombase-admin commented 9 years ago

Actually, I remember now, I think htis is culmulative,

Yep, the "immunofluorescence evidence" and "RNA protection assay evidence" counts come from previously loaded gene_ex annotations

BUT the totals are the same every time. it seems to have changed so that now it is just showing the Phenotype totals maybe???

It looks that way but there are changes in each table. eg. the "Non-traceable Author Statement" count changes between the first two and the second two tables. "Inferred from Direct Assay" changes in all the rest.

Shall I close this?

Original comment by: kimrutherford

pombase-admin commented 9 years ago

I still don't get it.

It says

1 | Inferred from Key Residues 3 | fusion protein localization evidence 6 | immunofluorescence evidence 15 | RNA protection assay evidence 36 | quantitative PCR 51 | reverse transcription polymerase chain reaction transcription evidence 94 | Cell growth assay 135 | Inferred from Expression Pattern 143 | reporter gene assay evidence 187 | Western blot evidence 213 | experimental evidence 239 | competitive growth assay evidence 586 | Northern assay evidence 725 | inferred from Reviewed Computational Analysis 750 | Inferred from Genetic Interaction 809 | Traceable Author Statement 1039 | Inferred from Physical Interaction 1373 | expression microarray evidence 1382 | Inferred by Curator 1470 | Inferred from Sequence Model 2353 | Inferred from Mutant Phenotype 2365 | Non-traceable Author Statement 2406 | Inferred from Sequence or Structural Similarity 3151 | Inferred from Direct Assay 5605 | Microscopy 6575 | Inferred from Sequence Orthology

Then reading go_proc.txt

most of the go process annotations will be IMP or IDA IC or TAS

but these stay the same as above:

2353 | Inferred from Mutant Phenotype 809 | Traceable Author Statement 3151 | Inferred from Direct Assay 1382 | Inferred by Curator

???

Original comment by: ValWood

pombase-admin commented 9 years ago

go_proc.txt is JUST the external file of NAS annotations, not all the GO BP annotations

Original comment by: mah11

pombase-admin commented 9 years ago

Diff:


--- old
+++ new
@@ -1,4 +1,3 @@
-

 http://curation.pombase.org/dumps/latest_build/logs/log.2015-01-23-04-40-03.gaf-load-output

Original comment by: ValWood

pombase-admin commented 9 years ago

ah OK

Original comment by: ValWood

mah11 commented 9 years ago

from the comments, looks like this turned out to be a non-issue