New Data Release on UKB-RAP: Olink Proteomics Data
The new tranche of Olink Proteomics data is now available in the UK Biobank Research Analysis Platform. This data is the result of the UK Biobank Pharma Proteomics Project (UKB-PPP), which characterized the plasma proteomic profiles of ~55,000 UKB participants. You can find more information on how we enabled visualization of Olink data on the UKB-RAP here.
You can use the refresh feature on UKB-RAP to access the data in your projects. This refresh feature allows researchers to use the existing projects with all the pipeline and logs without having to create a new project.
The RAP documentation has been updated with the release.
Comments
14 comments
Hi, I just wanted to know if there is any way to export "olink_data table" data as a csv file? in which there are an id column plus other columns with NPX values for each individual.
It not easy to import names of the proteins ( ~1000 ) one by one from the dashboard.
We will see what would be the best solution for this and include it as part of training on June 1. Meanwhile, if you have the list of all field id, you could use table exporter to export all fields you need from a file of field id rather than list each of them individually.
Thanks, would you please explain a bit more in detail how to use table exporter to extract multiple fields from proteomics data? I tried it a few times but did not work. For example I list "ACY1;Aminoacylase-1" in a filed name file but it says "Invalid characters found in field names on line number(s) 1 of the input.'"
The name you mention is field title, not field name. Field name is a number in case. Even better, you can use option File containing field name (second option)
You may also find this useful. https://community.dnanexus.com/s/question/0D5t000004SBm0eCAD/query-of-the-week-1-export-phenotypic-data-to-a-file
I would like to join the June 1 training. Can you please share the link for the training? Going forward, how can I learn about upcoming webinars and training sessions?
Here's the link: https://community.dnanexus.com/s/question/0D582000000fQAjCAM/webinar-june-1-analyzing-the-uk-biobank-proteomics-data-on-the-uk-biobank-research-analysis-platform
You can find all our upcoming webinars in the announcements tab: https://community.dnanexus.com/s/topic/0TOt0000000bunaGAA/announcements
And hear about them via email by joining our newsletter: https://share.hsforms.com/1amzIeTAmQca6h8TeD0CCvAcdds5
Thank, could you please offer the List of Field Names for All Proteins so that we can download all the proteomic data ?
This is answered in a separate post here: https://community.dnanexus.com/s/question/0D582000001ewWWCAY/could-you-please-offer-the-list-of-field-names-for-all-proteins-so-that-we-can-download-all-the-proteomic-data-
List of Field Names for All Proteins: https://github.com/dnanexus/UKB_RAP/blob/main/proteomics/field_names.txt
How import O-link data (npx values)
Video instructions here: https://youtu.be/Xn9J0X6plVM?t=758
Github with proteins names: https://github.com/dnanexus/UKB_RAP/blob/main/proteomics/field_names.txt
Location of slides (Same a video as slide 17-21 have the inof you want ): https://community.dnanexus.com/s/question/0D582000000fQAjCAM/webinar-june-1-analyzing-the-uk-biobank-proteomics-data-on-the-uk-biobank-research-analysis-platform
There are about 1500 protein across 53,000 people inject table take over 24 hours
To ingest table use the table exporter tool. Use tool as instructed in video, but instead of using a file to detail field names use "Advanced options" and enter in field names. Copy and paste the protein names from the above github link into Field names.
I was able to download the dataset using entity name as was described in the documentation. I just have a question. Is proteomics in the same blood assay category as NMR metabolomics or is it considered as a different category. In other words, it is a platform-based assay?
@UK Biobank DA Team?
The proteomics data is in Cost Tier d2 o2 s2, see Showcase field 30900, https://biobank.ndph.ox.ac.uk/showcase/field.cgi?id=30900,
The NMR metabolomics data is in Cost Tier d2 o1 s2, see Showcase field 23475, https://biobank.ndph.ox.ac.uk/showcase/field.cgi?id=23475.
So, the metabolomics data can be accessed by Tier 1 projects, so long as they access it Online (on the RAP) and do not download it.
The proteomics data can only be accessed by projects with Tier 2 or Tier 3.
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