EcoGene no longer maintained

[kimrutherford]

https://github.com/geneontology/go-site/commit/b8a34346f92a8fc7e1fe62bc40d47c33ed7a924d#diff-20c49b5866419d3b2e72f80936960031

I noticed because it has been removed from GO.xrf_abbs so we can't link to it anymore.

[ValWood]

Do we have any links to EcoGene?

[kimrutherford]

There are only a handful, ~6 in the contig files.

from chromosome3.contig:

with=EcoGene:EG14102

https://www.pombase.org/gene/SPCC4G3.17

[ValWood]

I will replace these tomorrow

[ValWood]

I only see this one?

grep "EcoGene" *.contig chromosome3.contig:FT db_xref=GO_REF:0000024; with=EcoGene:EG14102;

[ValWood]

I only see this one in the gaf too. Please reopen if there are some more...

[mah11]

case differences (which I guess were getting corrected automagically somewhere in the pipeline)

chromosome1.contig

• [x] FT /GO="aspect=F; term=DNA-3-methyladenine glycosylase FT activity; GOid=GO:0008725; evidence=IGI; FT db_xref=PMID:8921872; FT with=ECOGENE:EG10986,ECOGENE:EG11222; date=20120830"

• [x] FT /GO="aspect=F; term=DNA-7-methylguanine glycosylase FT activity; GOid=GO:0043916; evidence=IGI; FT db_xref=PMID:8921872; FT with=ECOGENE:EG10986,ECOGENE:EG11222; date=20120830"

• [x] FT /GO="aspect=F; term=tRNA(Ile)-lysidine synthase; FT GOid=GO:0032267; evidence=ISO; db_xref=GO_REF:0000024; FT with=ECOGENE:EG13357; date=20060922"

chromosome2.contig

• [x] FT /GO="aspect=P; term=histidine biosynthesis; FT qualifier=heterologous_system; GOid=GO:0000105; FT evidence=IGI; db_xref=PMID:8299169; with=ECOGENE:EG10451; FT date=20130412"

• [x] FT /GO="aspect=F; term=phosphoribosyl-AMP cyclohydrolase FT activity; qualifier=heterologous_system; GOid=GO:0004635; FT evidence=IGI; db_xref=PMID:8299169; with=ECOGENE:EG10451; FT date=20130412"

chromosome3.contig

• [x] FT /GO="aspect=P; term=pyrimidine nucleotide metabolic FT process; GOid=GO:0006220; evidence=ISO; FT db_xref=GO_REF:0000024; with=EcoGene:EG14102; FT date=20190129"

[ValWood]

Thanks!

[mah11]

grep -i ftw!