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Olink-Proteomics / OlinkRPackage

Olink R package: A collection of functions to facilitate analysis of proteomic data from Olink. The goal of this package is to help users extract biological insights from proteomic data run on the Olink platform.
GNU Affero General Public License v3.0
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PRIDE Archive integration with Olink #281

Closed ypriverol closed 1 year ago

ypriverol commented 1 year ago

I'm the team coordinator of PRIDE team (www.ebi.ac.uk/pride/), the largest proteomics database, part of ProteomeXchange. We have multiple users asking us to submit Olink data to PRIDE, something is not yet supported. I found this repository from Olink open in github and want to contact you for help.

We are modeling now how in PRIDE, how Olink data should look like, this is the first prototype: 

Olink:
RAW data:
         .bcl: raw data

Configuration Files:
         .plt: Detector setup file (.plt) from[ https://www.olink.com/members-site/](https://www.olink.com/members-site/) (which PLT file to use is stated on the lot configuration sheet)

Search results:
         .xlsx/txt: search results and quantification results in Excel files
Examples:
          https://figshare.com/articles/dataset/olink_ChipRun_IIM_raw_data/19367111

These are the requested files we are planning to ask the submitters for the community to be able to reproduce the results. Can you give us some feedback or help us about which data we should ask.

Thanks a lot in advance. Yasset

klevdiamanti commented 1 year ago

Hi Yasset,

Thank you for getting on touch with us. This is an important topic that might require involvment of a few stakeholders. Would you mind sending an email so that we (the Olink DS team) and other parties can be involved in the dicussion?

Best, Klev

ypriverol commented 1 year ago

yperez@ebi.ac.uk

Thanks in advance

kathy-nevola commented 1 year ago

Closing issue since conversation has moved to email.