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RNAcentral / rnacentral-webcode

RNAcentral website source code
https://rnacentral.org
Apache License 2.0
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searching on PomBase identifiers #417

Open ValWood opened 5 years ago

ValWood commented 5 years ago

SPSNORNA.29 search doesn't work? or sno52, even though this has been around for a while: https://www.pombase.org/gene/SPSNORNA.29

http://fungi.ensembl.org/Schizosaccharomyces_pombe/Gene/Summary?g=SPSNORNA.29;r=I:339548-339642;t=SPSNORNA.29.1

and is in the submission from a couple of years ago https://www.ebi.ac.uk/ena/data/view/CU329670

ValWood commented 5 years ago

The reason I was looking was that I was trying to see if our GO data was linking up with the entries in RNA central.... I wasn't able to find any.

How do you get the GO data? Do you pick it up from the GO consortium, or do we need to submit that directly too?

Val

AntonPetrov commented 5 years ago

@ValWood Thank you for pointing out this example. We do have a URS for the sno52 sequence but the PomBase xref has never been imported. We are investigating why.

blakesweeney commented 5 years ago

Hi, thanks for pointing the GO term issue out.

GO data is picked up from QuickGO (https://www.ebi.ac.uk/QuickGO/). It seemed to be a source of a broad range of annotations. I used their search a bit to see if I could find that example you provided and they don't seem to have it, which is why we don't have your annotations. I'm not certain where they get their annotations from. You provide GO annotations in the same format that QuickGO does so I can import your mappings as well.

You can also consider sending them to QuickGO as well. QuickGO's GO annotations for ncRNA are based off of RNAcentral identifiers, so you would have to map your annotations to RNAcentral identifiers.

ValWood commented 5 years ago

I could not see any pombe sno/sn RNA, but not to worry as the Json file will fix this.

ValWood commented 5 years ago

@tonysawfordebi which RNAs get included in QuickGO?

ValWood commented 5 years ago

QuickGO's GO annotations for ncRNA are based off of RNAcentral identifiers, so you would have to map your annotations to RNAcentral identifiers.

Actually I see. I don't think this is sustainable. It would be a lot of work for all of the MODs as we would need to get the mapping. Ass RNA central already has the mapping, and this will be required across species it would be better to get the annotation from the GO database and map it to RNA central identifiers. The GO database is really the primary repository for GO annotation anyway.....

ValWood commented 5 years ago

..although we will require a mapping of PomBAse to RNA central to add external links from our gene pages. Is this available?

AntonPetrov commented 5 years ago

The mapping between all member databases and RNAcentral ids is available on FTP. For example, here is the PomBase mapping: ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/id_mapping/database_mappings/pombase.tsv