Including with/from in GO annotation

[uliboehme]

The with/from part in the GO annotation is missing. In the GAF file, the with/from annotation is shown in column 8. For more information on column 8, please see the following link: http://www.geneontology.org/page/go-annotation-file-gaf-format-21

In PlasmoDB the with/from part is shown as Support for Evidence Code assignment. Here is an example: http://plasmodb.org/plasmo/app/record/gene/PF3D7_1207300#GOTerms

The with/from annotation can either be a UniProt link, a GeneDB link, InterPro ID, Pfam ID or a link to TMHMM. Here is an example for TMHMM. http://www.genedb.org/gene/PF3D7_0721500

[magnusmanske]

These should all be working in dev now, example: https://genedb.dev.sanger.ac.uk/#/gene/PF3D7_0721500 Items will be updated with the next run.

[uliboehme]

HI Magnus,

Thanks for looking into this. I can see the link to TMHMM for your example. Thanks!

Should the with/from also show up on other genes on genedb-dev? I cannot see it for example for RH5. This gene binds to various other proteins, those gene IDs should show up in the with/from column. You can see the with/from on PlasmoDB (it is listed as support for evidence code assignment). http://plasmodb.org/plasmo/app/record/gene/PF3D7_0424100#GOTerms

I don’t see this on genedb-dev. https://genedb.dev.sanger.ac.uk/#/gene/PF3D7_0424100

Would be great if you could let me know if I’m looking in the wrong place.

Thanks, Uli

On 27 Feb 2019, at 10:56, Magnus Manske notifications@github.com wrote:

These should all be working in dev now, example: https://genedb.dev.sanger.ac.uk/#/gene/PF3D7_0721500 https://genedb.dev.sanger.ac.uk/#/gene/PF3D7_0721500 Items will be updated with the next run.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_magnusmanske_genedb-5Fwd_issues_10-23issuecomment-2D467817923&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=af4zXwQtKNLvVIiDVaurRw&m=o80MgTKNyJNlOZHuLZoXVoXK6oAPwGMyDB-bTvXigWs&s=-8ChmGFQ5eYb920u_ZlRSAXl-7nQ1Sh0BnxDn7Qr3hc&e=, or mute the thread https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AX76FJ7OiA3LFwNMG-5FAoBLJ77TIdoiWuks5vRmRmgaJpZM4ZID5j&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=af4zXwQtKNLvVIiDVaurRw&m=o80MgTKNyJNlOZHuLZoXVoXK6oAPwGMyDB-bTvXigWs&s=JslePWVwmAkyBUZhBvlpav1J4LSv812mNsqGELXj8vg&e=.

-- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.