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Ancillary Study's Study Specimens Sample Set doesn't exists

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Ancillary Study's Study Specimens Sample Set doesn't exists Anthony Corbett  2013-04-05 13:24
Status: Closed
 
I'm using 12.3 and I thought I saw some enhancements coming in 13.1 for creating ancillary studies, not sure if these were some of them.

When an ancillary study was created I noticed two things:

1. All Specimens from the Specimen Repository were copied into the ancillary study for those participants that were selected. Is there a way to filter those to only a select few vials?

2. For all specimens that show up in the specimen repository the shadow Sample Set "Study Samples" does not exist. This is how I'm currently resolving Material RowIds for inputs to custom assays.
 
 
Anthony Corbett responded:  2013-04-10 09:25

For #2 above this creates other big issues, namely the following:

1. New assay data imported with the Ancillary Study as the Target Study can't properly link SpecimenId column to the SpecimenDetails to customize the view to include the ParticipantId or SequenceNum.

2. Along the same lines, resolving ParticipantVisit for copy to study doesn't work either.

See attached screenshots of both issues.

Thanks,

Anthony
 
adam responded:  2013-04-10 10:50
As for #1 in your original post, we recently implemented a "Specimen Study" capability that lets you create a child study (much like an ancillary study) from a specimen request. The filtering is driven by the specimens in that request... the resulting study will include only those specimens plus dataset rows & groups associated with the associated participants. This is currently an experimental feature that needs to be enabled via the admin console.

#2 sounds like a bug... the ancillary study is apparently not resolving the samples query to the right folder; I'll open an issue to track this. Several institutions are continuing to fund improvements in the ancillary study / study publication area, though I don't think any of them have encountered your issue.

Adam
 
Dave Bradlee responded:  2013-11-06 08:59
Hi Anthony,

I've just looked at Issue 17603, which Adam created from this. In 13.3, the original problem (Study Samples does not exist in ancillary study) was fixed. I observed by copying assay result to an ancillary study via copy-to-study and going to schema browser to accessing Study Specimens.

For the subsequent issues (the screenshots), if you could give more specific repro steps I could see if those are fixed or what I need to do to fix. Are SpecimenId, ParticipantId and/or SequenceNum supplied in the imported assay data or selected during copy-to-study?

Thanks.

Dave