[Pathway Discussion]: WP5321 and WP5122 are annotated to same pathway - missing description

[danidi]

The description of WP5122 is only one sentence, while there is a longer text shown on the old page https://classic.wikipathways.org/index.php/Pathway:WP5122.
See #169 for full discussion.

[rama289]

Also, several pathways like WP5124 have no description now, after the last update. Can some one please rectify this? thank you

[khanspers]

I made a small change too the pathway, which will trigger it (https://www.wikipathways.org/pathways/WP5122.html) to be updated during the daily sync. This should fix the description.

[khanspers]

Reopened this, since it seems there is a larger issue with missing/incorrect descriptions. I'm investigating.

[khanspers]

I checked about 20 other pathways that were edited in the same update as WP5124, and none of them had the same issue with description. So maybe its an isolated issue. @rama289: Please add the WPIDs for any other pathways that have the same problem with the description.

[rama289]

I found some who have problem with description: WP4718, WP4153, WP4719, WP4720, WP1603, WP5122, WP4726.
I don't know if they are work in progress or the description is missing because of some technicality. Hope it helps

[khanspers]

The problem with WP1603 was introduced in a recent update. The remaining pathways all have the same issue; it appears the description has been mismatched with classic for some time. I'm making the necessary changes to fix these issues.

[rama289]

Thank you so much. I only checked pathway lists for Homo sapiens. If it is happening often with db updates, maybe a systematic search to fix this issue for all pathways would be good.

[danidi]

@egonw Do you have a test that checks for large differences in the pathway description between versions? Might be good to catch potential errors.

[danidi]

I'm wondering if the shown one sentence description is an old title that was modified, rather than a description? Even the first description from this pathway which was a one sentence placeholder had a different wording than the currently shown description.
The description is currently still showing the one sentence only. If that was fixed by the update that was triggering the daily sync, it is now again showing it incorrectly.

[egonw]

@egonw Do you have a test that checks for large differences in the pathway description between versions? Might be good to catch potential errors.

No, I do not. The current curation stack works on the active set, and not a history. This is something we can do perhaps with the upcoming PR system, and something we did talk about in the past. it's also being done for source code, so why not for GPML too.

[egonw]

I'm wondering if the shown one sentence description is an old title that was modified, rather than a description?

Okay, thanks for bringing this up. I went into the RDF and found that WP5122 actually has two descriptions and then looked up the GPML source. And, yes, the GPML of WP5122 also turns out to have to descriptions. The classic website uses the first GPML description, and the new website the last, it seems.

The GPML snippet:

  <Comment Source="WikiPathways-description">Prostaglandins are active lipid molecules that are shown to have a great impact on cellular senescence (Wiley et al., 2021). Prostaglandins are derived from arachidonic acid, which is cleaved by the enzyme cytosolic phospholipase A2 (cPLA2
) from the membrane phospholipids (Yang et al., 2011). 

The cyclooxygenase 2 (COX-2)-prostaglandin E2 (PGE2) pathway takes part in the induction, as well as the maintenance of senescence. COX-2 is the inducing enzyme which causes the conversion of AA into PGH2 and PGG2, which are then readily converted into PGF2⍺, PGD2, PGE2, PGI2, and Tx
A2 through prostaglandin synthases (Cormenier et al., 2017; Martien et al., 2013). The produced active prostaglandins can then act on intracellular receptors and trigger a downward signalling cascade, leading to the stimulation or inhibition of cAMP or the stimulation of Ca2+. The cA
MP-dependent pathway leads to the stimulation of the insulin-like growth factor binding protein 5 (IGFBP5) production, which then also activates p53. P53 activation reinforces senescence by stimulating the expression of COX mRNA, thus creating a positive feedback loop (Yang et al., 2
011).

Two important active prostaglandins, namely dihomo-15d-PGJ2 and 15d-PGJ2 are highly elevated in senescent cells and induce COX-1 and 2, PTGES and PTGDS production through the activation of RAS and subsequently p53, reinforcing the positive feedback loop. Dihomo-15d-PGJ2 is the most h
ighly elevated senescence-associated prostaglandin and is produced by the elongation of arachidonic acid into adrenic acid, which is then enzymatically converted to yield the prostaglandin. 15d-PGJ2 on the other hand is produced through the dehydration of the active prostaglandin PGD
2. In addition, RAS stimulates the secretion of SASP factors, which can consequently affect surrounding cells (Wiley et al., 2021).

Leukotrienes play an important role in the pathogenesis of inflammation. Just like prostaglandins, leukotrienes are synthesized from arachidonic acid that was cleaved from the membrane phospholipids (Wiley et al., 2019). ALOX12, ALOX15, ALOX5AP, LTC4S, LTA4H, ALOX15B and ALOX5, which
 are enzymes that conversion of arachidonic acid to either leukotriene A4 (LT4A) or Arachidonic acid 5-hydroperoxide (5-HPETE), are upregulated in senescence (Wiley et al., 2019; Häfner et al., 2019). The produced LTA4 can be converted into LTB4 or LTC4. LTC4 can then be consecutivel
y cleaved into LTD4 and LTE4 (Suryadevara et al., 2020). All the mentioned leukotrienes are increased in cellular senescence and are thought to be part of the SASP (Lin &amp; Xu, 2020).

LTD4 is of particular importance in cellular senescence due to its increased interaction with the cysteinyl leukotriene receptor 1 (CysLT1R) (Wei et al., 2018; Song et al., 2019). This interaction has various consequences, such as the release of intracellular Ca2+, an increase of p21
 and it also inhibits sirtuin 1 (SIRT1). SIRT1 regulates the cell cycle by inhibiting the phosphorylation of p53 and the release of various cytokines (Wei et al., 2018).  Therefore, it increases the release of pro-inflammatory cytokines and induce cellular senescence via the activati
on of p53 (Song et al., 2019).

ALOX5 contributes to an increase in reactive oxygen species (ROS) (Catalano et al., 2005; Menna et al., 2010). These ROS are thought to activate p53 which binds to ALOX5 and further increases its action (Häfner et al., 2019). Moreover, ALOX5 uses Ca2+ as a cofactor and its increased 
intracellular concentration further promotes ALOX5's action (Menna et al., 2010). LTB4 is also stimulates the production of ROS. ALOX5 then stimulates the phosphorylation of p53 and activates p21 (Menna et al., 2010; Catalano et al., 2005). This then causes the dephosphorylation of t
he retinoblastoma protein (RB1). As a consequence, senescence is induced (Catalano et al., 2005).
</Comment>
  <Comment Source="WikiPathways-description">Prostaglandin pathway in senescence.</Comment>

[danidi]

@rama289 short update: we identified in total 60 pathways with mismatched description, thank you for bringing this up! I've corrected WP5122 and hopefully this time it shows up correctly after the daily sync. Other pathways will follow.