Annotation Guidance links from QuickGO broken

geneontology / geneontology.github.io

Repository for storing GO documentation, directly available through the general GO site

http://geneontology.org

MIT License

6 stars 10 forks source link

Annotation Guidance links from QuickGO broken #173

Closed suzialeksander closed 2 weeks ago

suzialeksander commented 5 years ago

On pages like https://www.ebi.ac.uk/QuickGO/term/GO:0030674, the link that previously went to Binding term considerations @ http://geneontology.org/GO.annotation.conventions.shtml#binding and now is broken

We need to find the doc, and let Quick GO know about new link. Searching for "binding guidelines" in the wiki goes to a 5 year old http://wiki.geneontology.org/index.php/Binding_Guidelines, I don't think this is the same as what we removed from the site?? ~~@pgaudet @vanaukenk do you recall what info the QuickGO site referred users to and if it exists on the wiki?~~

suzialeksander commented 5 years ago

Ok, it's here: https://web.archive.org/web/20181127144426/http://www.geneontology.org/page/go-annotation-conventions#binding

Is this on the wiki anywhere? I don't believe it is

suzialeksander commented 5 years ago

This documentation seems more in depth than what we planned on putting on the website, but I don't know that we had wanted to drive external traffic (from QuickGO) to the wiki. Are there users that would access 'annotation guidance' links through QuickGO that aren't curators though? Any arguments against having this doc on the wiki? @pgaudet @vanaukenk

pgaudet commented 5 years ago

@alexsign how are these added in QuickGO ?

@kltm Do you know if we have back up of those pages anywhere ?

The best replacement I know of would be this: http://wiki.geneontology.org/index.php/Annotating_binding but it would be great to look at the previous version of the website to see how it compares.

Thanks, Pascale

kltm commented 5 years ago

@pgaudet The Wayback Machine is probably a good place to start. If necessary, we could spin up a Drupal again, but that would take some fiddling.

pgaudet commented 5 years ago

Thanks @kltm

@alexsign this is where the Binging guidelines are now: http://wiki.geneontology.org/index.php/Annotating_binding

You probably also need to update: http://wiki.geneontology.org/index.php/Annotating_regulation http://wiki.geneontology.org/index.php/Annotating_downstream_processes http://wiki.geneontology.org/index.php/Annotating_ligand-receptor_pathways http://wiki.geneontology.org/index.php/Response_to_x_annotation_guidelines http://wiki.geneontology.org/index.php/Apoptosis_Curation_Manual http://wiki.geneontology.org/index.php/MicroRNA_GO_annotation_manual

Are there other such links ?

Thanks, Pascale

alexsign commented 5 years ago

Hi @pgaudet @ggeorghiou, I'm tagging George to it because the annotation guidance maintained by curators through Protein2GO.

ggeorghiou commented 5 years ago

These are the guidelines we currently have:

pgaudet commented 5 years ago

AFAIK the geneontology.org links are dead; can you please check ?

Thanks, Pascale

ggeorghiou commented 5 years ago

They are indeed dead.

pgaudet commented 5 years ago

Can you transfer to the links I listed above (https://github.com/geneontology/geneontology.github.io/issues/173#issuecomment-510368131) ?

ggeorghiou commented 5 years ago

Working on replacing the obvious ones now but we are missing some (like annotating to transcription factor activity, Describing enzyme functions that catalyse multi-stage reactions ). If I need to make new guidelines, I need to know how they have to be propagated and what to place in the other fields that are in the pictures above.

pgaudet commented 5 years ago

For transcription we have this:

https://docs.google.com/presentation/d/1hOBMnpHbGyKsOJi-Ah3xhAavzOg2RgM4AXRdGbF8A6M/edit#slide=id.p1

Not sure about the multistage reactions; I think we just give multiple GO annotations ?

suzialeksander commented 2 weeks ago

closing, all mentioned links seem to be addressed at QuickGO