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geneontology / go-releases

Tasks and notes for monthly GO releases
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Data exchange status of contributing groups #96

Open pgaudet opened 3 weeks ago

pgaudet commented 3 weeks ago

Google spreadsheet for tracking status: https://docs.google.com/spreadsheets/d/1Ph7w-dLAFNJJY3-8i5kgDRstBedg9a8zVmHbVyWgK_I/edit?gid=1076042544#gid=1076042544

Folder with individual files https://drive.google.com/drive/folders/13UHsK6Q3VLAqzJ8AgxfIc8tjurMJb7Gv

pgaudet commented 3 weeks ago

MGI - discussed with @LiNiMGI the GOA syntax error file The most important problem is 3800 unmapped identifiers, for eg: MGI:5792253 It's in AmiGO: https://amigo.geneontology.org/amigo/gene_product/MGI:MGI:5792253 but he link to MGI doesn't work

Li sees it in the MGI internal server, but not on the public server.

@LiNiMGI will investigate these genes.

LiNiMGI commented 3 weeks ago

Seems like the reason for "the link to MGI doesn't work" is due to MGI public site was down, it's working now.

For the 3800 unmapped identifiers, according to MGI Feature Type: antisense lncRNA gene 15 lncRNA gene 2682 sense intronic lncRNA gene. 2

miRNA gene 9 rRNA gene 4 snRNA gene 2 SRP RNA gene 1 tRNA gene 432 unclassified non-coding RNA gene 37

complex/cluster/region. 10 gene segment 36

polymorphic pseudogene 5 pseudogene 40 unclassified gene: 250 protein coding gene 334 (most of them are predicted genes; a few are protein coding genes without protein sequence information)

Please see attached spreadsheet for details. syntax check mouse unmapped identifiers.xlsx