A small number of rows where gene name, symbol and feature type have "no value"

[ValWood]

[ValWood]

@kimrutherford
@manulera

[kimrutherford]

I get the same list with this query:

<query model="genomic" view="Gene.primaryIdentifier Gene.secondaryIdentifier Gene.symbol Gene.name Gene.length Gene.organism.shortName" constraintLogic="(A and B)" sortOrder="">
   <constraint path="Gene.length" op="IS NULL" code="B"/>
   <constraint path="Gene.organism.shortName" value="S. pombe" op="=" code="A"/>
</query>

[kimrutherford]

I'm investigating (pombase/pombase-chado#967) why we export the transcript ID "SPAC1556.06.1" as an exact synonym for "SPAC1556.06" in the JSON file for PombeMine. But it might just be a coincidence that it's in this list.

• SPAC1F12.03c and SPAC4H3.12c aren't current PomBase identifiers. Those genes were removed sometime in the past. (Details: https://www.pombase.org/status/new-and-removed-genes)

  • Ensembl Genomes has SPAC4H3.12c still: https://fungi.ensembl.org/Schizosaccharomyces_pombe/Gene/Summary?g=SPAC4H3.12c
  • SPAC1F12.03c isn't in Ensembl Genomes.

• SPBC28F2.11 is a current PomBase gene. There are two genes with that DB identifier in PombeMine. I'm not sure why they haven't merged.

• SPBC8E4.02c is a synonym of SPNCRNA.9001 in PomBase because two genes were merged in the past. In PombeMine there is a gene object for SPBC8E4.02c and one for SPNCRNA.9001.

  • Ensembl Genomes has SPBC8E4.02c but not SPNCRNA.9001

• SPCC548.03c.1 and SPCC548.03c.2 are transcript IDs.

[kimrutherford]

I thought we only load genes from PomBase?

They will be loaded from any source that has gene data.

I should have done this earlier. Here is the result of querying PombeMine for the gene identifier and the DataSet that the identifier came from:

identifier	DataSet
Q9H9V9	GO Annotation data set
SPAC1556.06.1	BioGRID interaction data set
SPAC1F12.03c	BioGRID interaction data set
SPAC4H3.12c	BioGRID interaction data set
SPBC28F2.11	cerevisiae-orthologs data set
SPBC8E4.02c	BioGRID interaction data set
SPCC548.03c.1	GO Annotation data set
SPCC548.03c.2	GO Annotation data set

[ValWood]

• https://beta.uniprot.org/uniprotkb/Q9H9V9/entry is a human entry, determine how this gets into pombe gene set

[ValWood]

• Contact BioGRID about:

• SPBC8E4.02c is now a synonym of -> SPNCRNA.9001 (there is no longer a protein coding orf for this ID)

• SPAC1F12.03c. removed; replaced by a nuclear mitochondrial pseudogene (NUMT) feature

• SPAC4H3.12c not protein-coding (of upstream region of snr62). No corresponding gene feature (but might be part of snr62 transcript)

• SPAC1556.06.1 is a transcript ID for an alternative transcript of SPAC1556.06

Also asked @kimrutherford not to load into PomBase
#51

[ValWood]

• SPBC28F2.11 | cerevisiae-orthologs data set

I don't understand this one. The S. c orthologs are parsed from the contig files and this isn't mentioned except as a systematic ID?

See query
#50

[ValWood]

• when I search UniPRrt for these isoforms I only get one entry
  Q9P3V0

Can you send the GOA GAF so that I can investigate further? (the alternative forms would be in the column "gene product form ID (column 17)

Addded to #51

[kimrutherford]

SPBC28F2.11 | cerevisiae-orthologs data set
I don't understand this one. The S. c orthologs are parsed from the contig files and this isn't mentioned except as a systematic ID?
Yep, I think that's one for InterMine to investigate. outdated

Can you send the GOA GAF so that I can investigate further? (the alternative forms would be in the column "gene product form ID (column 17)

Here's the pombe and japonicus lines from the GOA GAF we load:
https://curation.pombase.org/kmr44/gene_association.goa_uniprot.pombe+japonicus-2022-04-01.tsv.gz

That's what PomBase uses, but PombeMine might be reading the XML file.

[ValWood]

identifier	DataSet
SPCC548.03c.1	GO Annotation data set
SPCC548.03c.2	GO Annotation data set

#51

[ValWood]

Sorry @danielabutano ! I thought this ticket was on our tracker whilst we tracked down the sources. So I can close this issue, more informative tickets. have been opened for the individual issues requiring action.

[ValWood]

BioGrid have mailed back. They have fixed the 4 issues at their end so these will disappear soon.