deustp01
commented
5 years ago Justin’s suggestion won’t break anything in the logic behind the data model and web display, but in my editorial opinion, if these entities are not yet involved in any of the molecular processes of the pathway shown in the diagram, but have only been placed in the diagram as curators’ notes to guide future annotation, then leave the annotations and the diagrams as they are now – creating an artificial “reaction” to link the entity to the reaction has the possibility of confusing human users and also of confusing overrepresentation analyses that will score hits on these entities as positives even though they are not in fact actually annotated as part of the pathway that is hit. My two cents. Peter
From: Justin Preece notifications@github.com Reply-To: PlantReactome/production-issues reply@reply.github.com Date: Thursday, August 22, 2019 at 6:31 PM To: PlantReactome/production-issues production-issues@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [PlantReactome/production-issues] Pathway diagram missing items: Reproductive meristem phase change (#43)
Missing from diagram: miR393a, RCN1, LAX1, LOG
Instances are not in slice 18. 9608760 9608694 9608693 9608698
Investigation thus far:
- our last slice says there were deleted items in the database that belong to that diagram. exactly the ones that we see missing: miR393a, RCN1, LAX1, LOG
- those items are present in gk_central
- what's different about them is that they have no referrers (i.e. no blackboxevent or reaction) for the slicing tool to pick up on and bring them along in the slice
- didn't we have a similar case with another pathway where you added blackbox events or somesuch to anchor the EWAS's and their regulatory arrows?
- can they be anchored to the pathways?
- i know several of those pathways are "placeholders". that also seems to be a contributing factor
- can you please compare to the EWAS elements that connect to pathway boxes in Regulatory Network of Nutrient Accumulation? those EWAS and arrows connecting to both a real pathway and a placeholder pathway are all present and accounted for. check that out, and see what you think. perhaps you can look into it and follow up with Peter if needed?
i think a solution could be to change the representation of those 4 EWAS by adding rxn's/bbe's as anchors. the slicing tool will not pick them up without some kind of referring event to be attached to.
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Missing from diagram: miR393a, RCN1, LAX1, LOG
Instances are not in slice 18. 9608760 9608694 9608693 9608698
Investigation thus far:
i think a solution could be to change the representation of those 4 EWAS by adding rxn's/bbe's as anchors. the slicing tool will not pick them up without some kind of referring event to be attached to.