NGS experiment documentation, export to GEO, custom assay types?

[Markus Suhr]

Hi all,

my colleagues and me currently try to prepare a primer for documenting (RNA -, ChIP- ) sequencing experiments in SEEK with the aim of automatically transferring the data to GEO. I read in one of the published articles about SEEK that this was already a possibility. But I have not been able to figure out how to achieve it so far.

Another problem we encountered is that some attributes would be better attached to an assay than to a sample type. In our use case, a set of attributes is exactly the same for all samples attached to an assay. Duplicating that information seems unnecessary (and from a user perspective, documenting in SEEK would not provide much benefit compared to sending the information to GEO directly). Is it possible to somehow define custom assay types with custom attributes attached? I understand that ISA format would allow for that?

Best regards,

Markus

[Alan Williams]

Hello Markus

At the moment two of our main workers are out of the office. Sadly I cannot answer your first question.  Can you point me at the article you mention.

It is possible to define custom assay types (under Administration -> Manage assay types). However, these would just put an entry in the assay_type ontology. I agree what you suggest would be a useful feature. For the moment, I think this information could be included in a SOP.

Sorry I cannot be more help. The two people should be back next week and may have better answers.

Alan

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From: seek4s...@googlegroups.com [seek4s...@googlegroups.com] on behalf of Markus Suhr [marku...@med.uni-goettingen.de]
Sent: 25 June 2018 08:15
To: SEEK
Subject: NGS experiment documentation, export to GEO, custom assay types?

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[Markus Suhr]

Am Dienstag, 26. Juni 2018 14:07:16 UTC+2 schrieb alan.r.williams:

 Can you point me at the article you mention.

Hi Alan,

it was not one of the original SEEK articles but another review [1] that mentioned SEEK would feature "upload to GEO" (Figure 3)

[1]

W. Wruck, M. Peuker, and C. R. A. Regenbrecht, ‘Data management strategies for multinational large-scale systems biology projects’, Brief Bioinform, vol. 15, no. 1, pp. 65–78, Jan. 2014.  https://academic.oup.com/bib/article/15/1/65/186751

 

Kind regards,

Markus

[Suhr, Markus]

Hi all,

could anybody provide further information regarding these questions?

[Katy Wolstencroft]

Dear Markus,

It is not currently possible to automatically submit data from SEEK to GEO. We suggested it as a possible future work extension in one of our papers, but other features took higher priority.

However, several of our templates for RNA data are based on GEO submission templates, with some added SEEK fields and embedded RightField annotation. This means that if you have used the templates, it should be easier to submit to GEO when you are ready to.

The templates are just a starting point. It is perfectly possible to define your own custom templates with custom attributes. The GEO formats seem to favour the duplication of information, rather than allowing changes to the structure of the input data though, so changes might result in more work when you do submit to GEO (see GEO submission instructions for further info here: https://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html#GAtemplates).

Some of our users submit their data directly to GEO and add it as an external link to SEEK instead (see example here: https://fairdomhub.org/data_files/1051). This prevents duplication of data storage, but still allows you to link your GEO data to other data stored in SEEK or in other repositories through the SEEK ISA structure. The disadvantage of doing it this way is that you can’t easily share it with other project members/collaborators before the GEO record is publicly released.

I am very happy to help if you want to design a custom template for your data. I go on vacation on Friday 3^rd August, but I am available before that.

Best wishes,

Katy Wolstencroft (k.j.wols...@liacs.leidenuniv.nl)

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