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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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obsoletion: transmission of virus #18601

Closed ValWood closed 4 years ago

ValWood commented 4 years ago

It isn't clear what this term is describing. The term has a parentage to "viral process"

It has 6 annotations: UniProtKB:P46934 NEDD4 involved_in GO:0019089 transmission of virus ECO:0000315 IMP PMID:15126635
9606 Homo sapiens BHF-UCL UniProtKB:Q62940 Nedd4 involved_in GO:0019089 transmission of virus ECO:0000266 ISO PMID:15126635
RGD:736612 10116 Rattus norvegicus RGD UniProtKB:Q8UZ11 UL36 involved_in GO:0019089 transmission of virus ECO:0000315 IMP PMID:15479829
33703 Suid herpesvirus 1 (strain Kaplan) AgBase
UniProtKB:Q8UZ12 UL37 involved_in GO:0019089 transmission of virus ECO:0000315 IMP PMID:15479829
33703 Suid herpesvirus 1 (strain Kaplan) AgBase
UniProtKB:Q9VAL0 Spase12 involved_in GO:0019089 transmission of virus ECO:0000315 IMP PMID:27383988
7227 Drosophila melanogaster UniProt UniProtKB:Q9VCA9 Spase22-23 involved_in GO:0019089 transmission of virus ECO:0000315 IMP PMID:27383988
7227 Drosophila melanogaster UniProt

the first one, for example Nedd4.1-mediated ubiquitination and subsequent recruitment of Tsg101 ensure HTLV-1 Gag trafficking towards the multivesicular body pathway prior to virus budding.

so human nedd4 should not be annotated to "viral transmission"

pgaudet commented 4 years ago

@pmasson55

pmasson55 commented 4 years ago

I have no idea what this term is about...The definition doesn't help much: "The transfer of virions in order to create new infection. " I don't think any host proteins should be annotated with this term...Some people use it to annotate host proteins while others use it for viral proteins... The definition should be more clear or the term should be deleted.

pgaudet commented 4 years ago

The whole branch should go: in AmiGO this are the annotations were have :

Thanks, Pascale

pgaudet commented 4 years ago

Dear all,

The proposal has been made to obsolete 'GO:0051821 dissemination or transmission of organism from other organism involved in symbiotic interaction' and children.

The reason for obsoletion is that those terms do not represent specific processes. If possible the genes should be annotated to more specific terms.

Annotation review requests are here:

There are 3 InterPro domains with mapping to GO:0019089 transmission of virus

InterPro:IPR007935 InterPro:IPR004917 InterPro:IPR007982 @happy-lorna

The terms are not present in any subsets.

Any comment may be added to the ticket:

https://github.com/geneontology/go-ontology/issues/18601.

We are opening a comment period for this proposed obsoletion. We’d like to proceed and obsolete this term on February 10th, 2020. Unless objections are received by February 10th, 2020, we will assume that you agree to this change.

Thanks, Pascale

pgarmiri commented 4 years ago

Hi, The 2 UniProt annotations have been reviewed and changed to GO:0050689 ' negative regulation of defense response to virus by host' Thanks, Penelope

pgaudet commented 4 years ago

Thanks !

ValWood commented 4 years ago

~Hi @pgarmiri Is that for https://www.uniprot.org/uniprot/Q9VCA9 I don't think these are "defense reponse"? It seems that the virus is hijacking the host secretory pathway? Here, we validated nine human genes required for flavivirus infectivity, and these were associated with endoplasmic reticulum functions including translocation, protein degradation, and N-linked glycosylation. In particular, a subset of endoplasmic reticulum-associated signal peptidase complex (SPCS) proteins was necessary for proper cleavage of the flavivirus structural proteins (prM and E) and secretion of viral particles.

pgarmiri commented 4 years ago

Hi @ValWood , good point! I have removed them now.

pgaudet commented 4 years ago

Hello,

Just a reminder that this term will get obsoleted next Monday (unless someone needs more time).

Thanks, Pascale

typhainepl commented 4 years ago

I've removed the GO terms from the InterPro entries.

pgaudet commented 4 years ago

Thanks @typhainepl