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pombase / pombase-chado

PomBase code for accessing Chado
MIT License
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log file og.2014-05-27-03-29-53.gaf-load-output confused by evidences #331

Closed pombase-admin closed 9 years ago

pombase-admin commented 10 years ago

reading go_comp.txt no taxon filter - annotation will be loaded for all taxa counts: count | value
-------+------------------------------------------------------------------------ 1 | fusion protein localization evidence 1 | Inferred from Key Residues 4 | immunofluorescence evidence 6 | RNA protection assay evidence 15 | quantitative PCR 24 | reporter gene assay evidence 37 | reverse transcription polymerase chain reaction transcription evidence 93 | Western blot evidence 159 | Inferred from Expression Pattern 191 | experimental evidence 239 | competitive growth assay evidence 373 | Northern assay evidence 728 | inferred from Reviewed Computational Analysis 913 | Inferred from Genetic Interaction 999 | Traceable Author Statement 1093 | Inferred from Physical Interaction 1365 | expression microarray evidence 1455 | Inferred by Curator 1512 | Inferred from Sequence Model 2491 | Non-traceable Author Statement 2507 | Inferred from Sequence or Structural Similarity 2521 | Inferred from Direct Assay 2933 | Inferred from Mutant Phenotype 4828 | Microscopy 6539 | Inferred from Sequence Orthology

includes evidences we don't use for GO

similarly reading go_proc.txt no taxon filter - annotation will be loaded for all taxa counts: count | value
-------+------------------------------------------------------------------------ 1 | fusion protein localization evidence 1 | Inferred from Key Residues 4 | immunofluorescence evidence 6 | RNA protection assay evidence

uses evidences we don't use for process.....

where do these come from?

v

Original comment by: ValWood

pombase-admin commented 10 years ago

where do these come from?

Sorry it's not clear, but those tables are cumulative totals rather than the totals for the data file just read in. I started logging the counts for debugging purposes and didn't make it obvious what it meant.

Original comment by: kimrutherford

pombase-admin commented 10 years ago

OK kind of makes sense where does this come from:

1 | fusion protein localization evidence

(I haven't seen it before but it might be useful for the Sophie Martin paper I am looking at. It isn't an option that we use in canto though...were is it in our data?

Original comment by: ValWood

pombase-admin commented 10 years ago

It's this annotation:

FT /controlled_curation="term=gene expression, protein level; FT annotation_extension=during(GO:0060274); FT qualifier=increased; evidence=ECO:0000124; FT db_xref=PMID:22646093; date=20140214"

from SPAC32A11.03c, ECO:0000124.

Original comment by: kimrutherford

pombase-admin commented 10 years ago

hmm that seems an odd experiment for fusion localization evidence will move that on the curator tracker

so the totals include all of the evidence codes read from the contigs to start off with?

Original comment by: ValWood

pombase-admin commented 10 years ago

so the totals include all of the evidence codes read from the contigs to start off with?

Yep.

Original comment by: kimrutherford

pombase-admin commented 10 years ago

Original comment by: ValWood