FB00000804 (Redo)

[robes]

This was the GEO dataset submitted before as just a link to GEO. We now have the data and a (geo) metadata spreadsheet.

data-staging:/home/vasu/GSE67985*

[robes]

I just took another look to refresh my memory. What we have are a .tar file with a batch of gzipped cel files. Then we have a GEO text / spreadsheet for their GEO metadata. What we can do is load the gzipped cel files. But the spoke will have to curate the metadata according to the facebase standards.

[crisaless]

https://www.facebase.org/chaise/record/#1/isa:dataset/RID=VX6

still no data files included

[bugacov]

I believe we decided that on datasets like this we'll just leave the dataset with the link to GEO.
@robes .... what do you think?
@BridgetDS ... do you think it will make sense to try to do additional curation on a dataset like this and upload the data files?

[BridgetDS]

We've just been leaving them on geo only, and adding the link to geo as a related dataset. Not sure if this will be confusing for users.

…

On Feb 5, 2020, 6:05 PM -0800, bugacov ***@***.***>, wrote: I believe we decided that on datasets like this we'll just leave the dataset with the link to GEO. @robes .... what do you think? @BridgetDS ... do you think it will make sense to try to do additional curation on a dataset like this and upload the data files? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

[robes]

Yes, we can just reference the GEO dataset. A good description of the dataset on FaceBase would be important but the files and data might as well remain where they’ve already been submitted. On 2/5/20, 6:05 PM, "bugacov" <notifications@github.com<mailto:notifications@github.com>> wrote: I believe we decided that on datasets like this we'll just leave the dataset with the link to GEO. @robes<https://github.com/robes> .... what do you think? @BridgetDS<https://github.com/BridgetDS> ... do you think it will make sense to try to do additional curation on a dataset like this and upload the data files? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#41>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABACCWVNB4U34YGCRDB2W3TRBNV7RANCNFSM4DITLPYA>.

[BridgetDS]

Note that these "GEO-only" datasets get flagged for curation issues:

[robes]

Good point. Let’s bring this up with Alejandro. He can adjust the curation QC rules so that we make these an exception to the normal expectations. On 2/7/20, 11:15 AM, "BridgetDS" <notifications@github.com<mailto:notifications@github.com>> wrote: Note that these "GEO-only" datasets get flagged for curation issues: [Image removed by sender. Screen Shot 2020-02-07 at 11 13 45 AM]<https://user-images.githubusercontent.com/14893197/74058463-f2788f80-499a-11ea-9f8a-a5c3f72ff904.png> — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#41>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABACCWRIAEKEC6ZYXOVUB6LRBWXLBANCNFSM4DITLPYA>.