Bos taurus pathways no longer in GMT

[Brad Sherman]

We have noticed that from the 20220110 to the 20220210 GMT release, 26 pathways have been removed for Bos taurus.  Looking into one of these, https://www.wikipathways.org/index.php/Pathway:WP1009, we do not see a revision in this timeframe that may have prompted the removal although the pathway does not appear to be approved.  Why have these pathways been removed?

Thank you for any help and this extremely useful resource.

Regards, Brad

WP1009:MAPK cascade
WP1026:One-carbon metabolism
WP1030:Selenium metabolism and selenoproteins
WP1037:p38 MAPK signaling pathway
WP1038:Vitamin A and carotenoid metabolism
WP1044:ErbB signaling pathway
WP1054:Polyol pathway
WP1061:Fatty acid beta-oxidation
WP3116:Ovarian infertility
WP3119:DNA damage response
WP3121:Physiological and pathological hypertrophy of the heart
WP3125:One-carbon donor
WP3129:Bladder cancer
WP3135:Trans-sulfuration and one-carbon metabolism
WP3143:DNA damage response (only ATM dependent)
WP3153:RANKL / RANK signaling pathway
WP3169:BMP signaling and regulation
WP3181:Nanoparticle-mediated activation of receptor signaling
WP3188:Liver X receptor pathway
WP3218:TFs regulate miRNAs related to cardiac hypertrophy
WP3225:Differentiation of white and brown adipocyte
WP3239:TP53 network
WP3258:PPAR-alpha pathway
WP3266:Glioblastoma signaling pathways
WP3269:Farnesoid X receptor pathway
WP3843:Vitamin A and carotenoid metabolism

[alex.pico]

Hi Brad,

All the pathways that were removed were automatically translated from human to cow and were not further curated.  We agree that these are valuable, but our system for keeping them up to date was broken. In fact, many were based on a 2013 conversion.  We are transitioning to a new and improved homology modeling system that will update the cow pathways each time its source human pathway is updated. A huge improvement!  And the homology content will be exported as GMTs as well for important use cases like yours.

I will prioritize generating a new cow GMT for you with the latest converted content. 

In the meantime, you can simply keep using the 20220110 GMT. The old content there wasn't being updated (by the old mechanism), so you are not missing anything by sticking with an older release.

I'll follow up with a handmade GMT for you soon.

 - Alex

[alex.pico]

Attached is an example of new GMT that includes curated Cow pathways, plus all the homology converted pathways from human that have 80% or more gene homology (see "PlusHomology" in filename). The WPIDs and URLs for human-sourced content will link to the human versions of the pathways online.

Let us know if this works for you. Our plan is to produce these augmented GMT files monthly and release them along side the curated content GMTs so users can choose what they want.

Cheers,

Alex

[alex.pico]

Note that there are cases where a pathway was converted from human (say, back in 2015) and then was modified by curators so it is retained in the "curated" collection, like https://www.wikipathways.org/instance/WP3203.  But the original human pathway also has been curated since that time (https://www.wikipathways.org/instance/WP2276) so a fresh conversion results in a pathway with additional datanodes. In the GMT file I provided, both the curated cow pathway and the newly converted one are present.  I suspect some users will want this (i.e., as many possible hits as possible), while other will just want to test the curated and converted collections separately.

What is your preference?

 - Alex