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pombase / pombase-chado

PomBase code for accessing Chado
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what to do when external annotation files use names which are now synonyms #246

Closed pombase-admin closed 2 years ago

pombase-admin commented 11 years ago

These genes no longer exist. http://www.pombase.org/status/new-and-removed-genes

can you let me know where they are referred to? Thanks Val

skipping annotation: can't find feature for: SPAC1F12.03c skipping annotation: can't find feature for: SPBC1348.13

Original comment by: ValWood

pombase-admin commented 11 years ago

As far as I can tell these do still exist, at least the ones I checked so far? (I think they are possibly all synonyms, arisen from merges?) Val

skipping annotation: can't find feature for: SPNCRNA.817 skipping annotation: can't find feature for: SPNCRNA.77 skipping annotation: can't find feature for: SPNCRNA.78 skipping annotation: can't find feature for: SPNCRNA.193 skipping annotation: can't find feature for: SPNCRNA.75 skipping annotation: can't find feature for: SPNCRNA.884 skipping annotation: can't find feature for: SPNCRNA.18 skipping annotation: can't find feature for: SPNCRNA.951 skipping annotation: can't find feature for: SPNCRNA.958 skipping annotation: can't find feature for: SPNCRNA.994 skipping annotation: can't find feature for: SPNCRNA.101 skipping annotation: can't find feature for: SPNCRNA.1341 skipping annotation: can't find feature for: SPNCRNA.1347 skipping annotation: can't find feature for: SPNCRNA.104 skipping annotation: can't find feature for: SPNCRNA.1380 skipping annotation: can't find feature for: SPNCRNA.1388 skipping annotation: can't find feature for: SPNCRNA.1486 skipping annotation: can't find feature for: SPNCRNA.106 skipping annotation: can't find feature for: SPNCRNA.1612 skipping annotation: can't find feature for: SPNCRNA.1652 skipping annotation: can't find feature for: SPNCRNA.1679 skipping annotation: can't find feature for: SPNCRNA.1098 skipping annotation: can't find feature for: SPNCRNA.64 skipping annotation: can't find feature for: SPNCRNA.125 skipping annotation: can't find feature for: SPNCRNA.489 skipping annotation: can't find feature for: SPNCRNA.1196 skipping annotation: can't find feature for: SPNCRNA.582 skipping annotation: can't find feature for: SPNCRNA.502 skipping annotation: can't find feature for: SPNCRNA.10 skipping annotation: can't find feature for: SPNCRNA.1254 skipping annotation: can't find feature for: SPNCRNA.1274 skipping annotation: can't find feature for: SPNCRNA.1291 skipping annotation: can't find feature for: SPNCRNA.1295 skipping annotation: can't find feature for: SPBTRNAASP.03

Original comment by: ValWood

pombase-admin commented 11 years ago

that flavor of message comes from loading the quantitative gene expression data

pombe-embl/external_data/Quantitative_gene_expression_data/

..and it does rather look like that loader isn't using gene/feature synonyms

Original comment by: mah11

pombase-admin commented 11 years ago

and it does rather look like that loader isn't using gene/feature synonyms

Yep, in most cases it only checks the systematic_id (uniquename in Chado) when loading. In some cases it checks the primary gene name too.

I can change it to use the synonyms as well if that's appropriate.

Original comment by: kimrutherford

pombase-admin commented 11 years ago

I can change it to use the synonyms as well if that's appropriate.

I think for now we should keep as is, as it alerted us to the fact that there are 2 lots of data for some genes.

In these issues we might need to handle on a case by case basis

we can discard the data for skipping annotation: can't find feature for: SPAC1F12.03c skipping annotation: can't find feature for: SPBC1348.13 as these are now nUMT's not genes

Original comment by: ValWood

kimrutherford commented 2 years ago

I think we should close this since it's so old.