Fix weird feature_cvtermprop source_file from GOA loading

kimrutherford commented 7 months ago

Value is "pipe:[250445082]"

ValWood commented 7 months ago

does this need reporting to GOA?

kimrutherford commented 7 months ago

It's a bug in the loading script when loading the GOA GAF. It should be a quick fix.

It's not urgent this value in Chado isn't used on the website. I'm the only person who looks it. :-)

kimrutherford commented 7 months ago

It's fixed for tonight's load. I'll check in the morning.

kimrutherford commented 7 months ago

This is fixed now.

This property is mostly for tracking down problems. We store the source for each GO annotation as a property of the annotation in Chado so it can be queried if needed.

The current list is:

from_curation_tool (the session ID and other details also stored for each annotation)
GO_ORFeome_localizations2.txt
PMID_20838651_gaf.tsv
PMID_22146723_gaf.tsv
PMID_26412298_gaf.tsv
PMID_27984725_gaf.tsv
chromosome1.contig
chromosome2.contig
chromosome3.contig
gene_association.goa_uniprot.pombe+japonicus.gz
legacy_go_annotations_from_contigs.gaf.tsv
mating_type_region.contig
pMIT.contig
pombase-prediction.gaf
snapshot.geneontology.org/pombase.gaf.gz
telomeric.contig

ValWood commented 7 months ago

Should contigs still be in the list? We don't load GO annotations from contigs anymore. They are all in the 'legacy' file

kimrutherford commented 7 months ago

There is still GO annotation in the contig files for multi-transcript genes.

ValWood commented 7 months ago

Of course.

pombase / pombase-chado

Fix weird feature_cvtermprop source_file from GOA loading #1164