Hi all,
I’m looking for advice on how best to download the entire Caenorhabditis elegans genome from WormBase in a format that I can open in Excel.
Ideally, I’d like: • One row per gene • One column with the gene name/ID • Another column with Wormbase's automated short description of gene see attached example for unc-1
Does WormBase offer this kind of table directly, or would I need to process a file myself (e.g., using BioMart, WormMine, or a REST API)?
Grateful for any tips, example scripts, or direct links to preformatted downloads.
Thanks so much!
I’d like: • One row per gene • One column with the gene name/ID • Another column with Wormbase's automated short description
You can go to : https://wormbase.org/tools/mine/simplemine.cgi
Select C. elegans. Under step 3 uncheck the box that says Set All Checkboxes. Then select boxes for Public Name and Concise description (and anything else you want). Finally click on All genes in this species.
You should get a table that looks like this
This is absolutely amazing!! Thank you for such a concise and helpful answer - that's precisely what I wanted! Do you know if there's any way for me to download/save/pull out an excel/data table from this web result? Thanks!!
I'd just set the download results as a tab-delimited file radio button, and try to import the resulting tab-delimited file (about 8MB, no problems during import). Don't forget to change the column type from General to Text to avoid surprise conversions.
Perfect, thank you! Worked like a charm.
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