Hello, I am trying to check Omop database files to extract the phenotypes of my interest. May I know how to access these databases to download the updated phenotypes?
Thank you so much
Regards
Akhil
When did you last refresh your data on the RAP? The OMOP data is new for the latest RAP version, so the copy of the data that is in your project area might not have it yet.
I refreshed it last month and started doing the same yesterday since the new data release. I will check once it is done. Where can I find these files ? Will it be in the bulk area?
Yeah, I was doing the same. I thought OMOP tables have been available since last month, as I recall an announcement during that time. Thank you very much for the information. I'm still waiting for the refresh; hopefully, it will be completed sooner.
I see. Where did you see the announcement? We just announce it this week. If we accidentally announce it too soon, we can look into fixing that if we know where it comes from.
I saw that in the UK Biobank data showcase release, available here (https://www.ukbiobank.ac.uk/enable-your-research/about-our-data/past-data-releases), not in the community announcements. I was under the impression that the data releases from UK Biobank and RAP are simultaneous. I will follow the community announcements moving forward.
I'm not sure I understand the questions, but let see if this is useful.
If you see 0%, the refresh isn't start yet and you are in the queue, so you should be able to export data out as tsv or csv and keep them on RAP. However, once the refresh start (different number than 0%), I would avoid it even if the platform allow you to. It's just that some data is being updated and I didn't want to have something in between two versions of data.
Download is a different function from export. You could download data out of UKB-RAP at any time as long as it's allowed by your research application.
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You would access OMOP the same way as other phenotypic data (Spark, dxdata, "dx extract_dataset", or Table Exporter).
https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/using-spark-to-analyze-tabular-data#database-tables
is it possible to do a sql query directly from the database instead of downloading?
Looks like i dont have access for that, how to request access for omop dataset?
@Chai Fungtammasan?
What is your tier of access? If you are eligible, you can ask for request from UKB data access team. @UK Biobank DA Team?
I believe I have tier 3 access.
When did you last refresh your data on the RAP? The OMOP data is new for the latest RAP version, so the copy of the data that is in your project area might not have it yet.
See updating dispensed data and data release versions
I refreshed it last month and started doing the same yesterday since the new data release. I will check once it is done. Where can I find these files ? Will it be in the bulk area?
No, there are no "OMOP" files in the Bulk folder. I haven't tried it myself, but I believe you need to use a Spark JupyterLab cluster, see https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/using-spark-to-analyze-tabular-data
@Akhil Pampana? Ondrej answered this above too.
After you see data release announcement, you need to always refresh or re-dispense a new project to get data that we announce.
Yeah, I was doing the same. I thought OMOP tables have been available since last month, as I recall an announcement during that time. Thank you very much for the information. I'm still waiting for the refresh; hopefully, it will be completed sooner.
I see. Where did you see the announcement? We just announce it this week. If we accidentally announce it too soon, we can look into fixing that if we know where it comes from.
I saw that in the UK Biobank data showcase release, available here (https://www.ukbiobank.ac.uk/enable-your-research/about-our-data/past-data-releases), not in the community announcements. I was under the impression that the data releases from UK Biobank and RAP are simultaneous. I will follow the community announcements moving forward.
Many thanks Akhil. This is very helpful for us. Let us know if you run into any issue with data once your refresh is finished.
If I want to download a dataset while refreshing using the older dataset we have, will I be able to do that?
I'm not sure I understand the questions, but let see if this is useful.
If you see 0%, the refresh isn't start yet and you are in the queue, so you should be able to export data out as tsv or csv and keep them on RAP. However, once the refresh start (different number than 0%), I would avoid it even if the platform allow you to. It's just that some data is being updated and I didn't want to have something in between two versions of data.
Download is a different function from export. You could download data out of UKB-RAP at any time as long as it's allowed by your research application.
I got the answer based on the response. Thank you for the information.
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