Monthly gmt files missing for some species

[Uku Raudvere]

Hello,

It seems that some species are missing the gmt files starting with the 20201110 release.

http://data.wikipathways.org/20201010/gmt/ contains the files:

wikipathways-20201010-gmt-Sus_scrofa.gmt

wikipathways-20201010-gmt-Equus_caballus.gmt

wikipathways-20201010-gmt-Populus_trichocarpa.gmt

The corresponding files are missing in http://data.wikipathways.org/20201110/gmt/ and http://data.wikipathways.org/20201210/gmt/.

I looked for, but didn't find, any notice of deprecation or announcement about removing these files. Were they removed deliberately? Will they return in future releases?

Best,

Uku

[Kristina Hanspers]

Hi Uku,

The missing gmts are due to an error, we are working to fix it. The data release will be updated. 

Regards,

Kristina

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[Alex Pico]

In the meantime, it would be great to know how you are using these. Frankly, I was starting to doubt our need to release these regularly for species that don’t actually see regular updates to the content. For example, Sus scrofa file is the same as it was a year ago. It would be helpful to learn about your real world use cases.

 - Alex

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[Uku Raudvere]

I'm very glad that it's just an error and the files will return. Thank you for looking into it!

As for my use case - I prepare quarterly releases of our functional enrichment analysis tool g:Profiler (https://biit.cs.ut.ee/gprofiler). We use the WikiPathways gmt files for some of our annotations.  It's great that we can refer to a particular release (e.g. 20201010) and point our users to particular archived releases (data.wikipathways.org for WikiPathways) for transparency. It's definitely useful that the files are officially part of a release even if they haven't changed. 

Uku

[Kristina Hanspers]

Hi Uku,

The missing gmt files are now back online, for November and December. 

Regards,

Kristina

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