ERROR in msigdb_v2023.2.Hs.xml file

[Charline Jnnt]

Hi, 

I want to download the latest version of the MSigDB (msigdb_v2023.2.Hs.xml.zip) from https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2023.2.Hs/ url but, when I download the file, unzip it, and try to open the .xml file, I get the following error: 

This page contains the following errors:

error on line 329 at column 333: Unescaped '<' not allowed in attributes values

Below is a rendering of the page up to the first error.

(same error when I import the file into R studio).

The error does not occur when using previous versions as the msigdb_v2023.1.Hs.xml.zip or the msigdb_v2022.1.Hs.xml file. 

Can this error be fixed ?

[Anthony Castanza]

Hi Charline,

Thanks for letting us know.

Our support for the XML file is quickly approaching end-of-life and we're encouraging everyone to move to the sqlite flat file or the json files that we provide now. I'd first suggest seeing if you can get the data you need from either of those - the json file is probably easiest to work with. That said if you can't get what you need out of either of those please let me know and I can bump a fix for this up the priority list.

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego

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[Charline Jnnt]

Hi Anthony, 

Thank you for your quick reply ! 

No problem, I used the json file instead of the xml format. 

Charline