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automate dbGap URL population #266

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shirey opened this issue Nov 18, 2022 · 1 comment
Open

automate dbGap URL population #266

shirey opened this issue Nov 18, 2022 · 1 comment
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@shirey
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shirey commented Nov 18, 2022

@icaoberg @pdblood We'll need the associated dbGap "experiment id", I think? We'll need this for existing datasets then for all future datasets as they are uploaded to dbGap. I thought that we worked out the URL pattern to use which includes the URL, but I'm not finding it recorded anywhere, so please remind me of that too.

Related issue which has been completed: hubmapconsortium/entity-api#282

@shirey shirey self-assigned this Nov 18, 2022
@shirey shirey added P I Infrastructure labels Nov 18, 2022
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shirey commented Dec 14, 2022

Putting this here so I don't forget:
HuBMAP Project In dbGap: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA671343
List of experiments from that project (link in "number of links" column next to SRA Experiments on above page): https://www.ncbi.nlm.nih.gov/bioproject/PRJNA671343
Link to an individual experiment from the list: https://www.ncbi.nlm.nih.gov/sra/SRX15196860[accn]

This last link is what we need to store as the dbgap_url for every dbGap registered dataset.

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