confused by some evidence codes described for GO data

pombase-admin commented 10 years ago

This file http://curation.pombase.org/dumps/pombase-build-2013-12-13-v2-l1/logs/log.2013-12-17-02-54-06.gaf-load-output

Has thisng like

reading go_comp.txt (SO THE GO COMPONENT FILE)

But then lists some evidences which we don't use with this ontology:

no taxon filter - annotation will be loaded for all taxa counts: count | value
-------+------------------------------------------------------------------------

 6 | RNA protection assay evidence
 7 | quantitative PCR
22 | reporter gene assay evidence
30 | reverse transcription polymerase chain reaction transcription evidence
61 | Western blot evidence

1365 | expression microarray evidence

2542 | Inferred from Sequence or Structural Similarity

3086 | Inferred from Mutant Phenotype 4828 | Microscopy

(23 rows)

Original comment by: ValWood

pombase-admin commented 10 years ago

I think Kim said those totals are cumulative, and it also looks like the first table of counts must already include GO annotations from the embl files (based on the numbers and on the fact that the embl files don't have a separate heading in that log).

Original comment by: mah11

pombase-admin commented 10 years ago

OK makes sense. well confusing but makes sense ;)

I forgot...

Original comment by: ValWood

pombase-admin commented 10 years ago

Sorry it's a bit confusing. I initially put those query results in the log so I could see at a glance that the totals were increasing after each input file was loaded.

Original comment by: kimrutherford

pombase-admin commented 10 years ago

Original comment by: ValWood

pombase-admin commented 10 years ago

OK, I remember now. That's fine. I just need to keep it in my head. v

Original comment by: ValWood

pombase-admin commented 10 years ago

status: open --> closed-works-for-me

Original comment by: ValWood

pombase / pombase-chado

confused by some evidence codes described for GO data #280