GeneDB issues

[pgaudet]

Problems with GeneDB

• GeneDB links updated but not implemented New link outs to GeneDB go-site#1779 New sources for GeneDB data, need to be added back into AmiGO go-site#1777
• As of the May 2022 release, L major and plasmodium links to UniProt, for eg https://amigo-staging.geneontology.io/amigo/gene_product/UniProtKB:Q8ID53 https://amigo-staging.geneontology.io/amigo/gene_product/UniProtKB:Q4Q1R1 it should link to EuPathDB, see New link outs to GeneDB go-site#1779
• PAINT uses UniProt IDs for Trypanosoma brucei brucei TREU927, so we have 2 entities annotated for the same gene for IBAs and for annotations coming from GeneDB: - http://amigo.geneontology.org/amigo/gene_product/TriTrypDB:Tb927.1.630:mRNA - http://amigo.geneontology.org/amigo/gene_product/UniProtKB:Q4GZF6

[pgaudet]

Once done, make sure Alex knows

[pgaudet]

Email exchange with Dr David Starns (He/Him)
VEuPathDB Annotation and Curation
2023-05-15

Dear Pascale,

Let me just introduce myself, I am a member of the Curation and Annotation team at VEuPathDB and after Achchuthan left the project I was referred to you on matters of Gene Ontology integration. We previously supplied files to the Gene Ontology via the Sanger FTP site with the GeneDB YAML configuration file. As GeneDB is now defunct we would like to update the YAML to represent curated GO files(GAF only presently) via VEuPathDB. We've just completed the development work to allow for this and was wondering whether you wanted us to contribute a new YAML file in the following directory for our curated Eukaryotic Pathogen and Fungal genomes?

https://github.com/geneontology/go-site/tree/master/metadata/datasets

Any direction on how to proceed would be wonderful.

Best Wishes,

Dave

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Dear Dave,

Thanks for getting in touch. Yes please either update the yaml file, or I can do it myself if you prefer. Note that we need a zipped file on your end.

Also, are you aware that GO and UniProt is having a hard time making links to VEuPathDB, because the different links are supposed to be created from the same namespace, see some explanation here:
geneontology/go-site#1779

I am happy to set up a call if you’d like more explanation on this one.

Best wishes,

Pascale

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Currently the files are not zipped so will have to talk to our infrastructure team in regard to that (probably Wednesday), I'll also have a look into the links with the infrastructure too. Sorry for the lack of communication, just trying to get on top of everything.

I'll have a look into the github issue and if there is anything I need more explanation with I'll take you up on that call. Will be great to be in synch with both GO and uniprot.

Best wishes,

Dave

[pgaudet]

2023-09-28

Emailed Uli

I am QC’ing the data for the next GO release, and there is an issue with the Plasmodium falciparum 3D7 IEA annotations, that are now more than 2 year old, so according to our practices, these annotations will be filtered out from the GO products, including AmiGO. This affects about 3,500 annotations, ie an overall drop of 20% in the Plasmodium falciparum annotations.

Uli:

Thanks for your e-mail and for letting me know about the IEA annotations. Unfortunately, we currently only run those predictions when the genome is being updated. We’ve been discussing to run this more frequently for all genomes. It is currently not clear though when this can be implemented.

[pgaudet]

GAF Files and links have been updated, see geneontology/go-site#2256 (comment)

We plan to add this in the release after the upcoming one, so we have some time to fix any issues that may arise.

[pgaudet]

Noting

• this data can be loaded in as-is GOC because we accept any ID space
• however GOA cannot load because VEuPathDB-Uniprot links are not available
• TO DO on the VEuPathDB side: the GAF files need to contain different namespaces for the different species for links to resolve correctly