encoding of binding regions in json?

[colin-combe]

the psi-mi json for CPX-1924 contains a feature like:

{
              "id": "16",
              "name": "psi binding region",
              "category": "bindingSites",
              "type": {
                "id": "MI:0117",
                "name": "binding-associated region"
              },
              "sequenceData": [
                {
                  "pos": "?-79",
                  "interactorRef": "uniprotkb_P28905",
                  "participantRef": "18"
                }
              ],
              "linkedFeatures": [
                "15"
              ]
}

as things are, this doesn't get displayed in ComplexViewer because the "pos": "?-79" isn't one of the eventualities it's prepared for.

This wasn't one of possibilities given in https://github.com/MICommunity/ComplexViewer/blob/master/src/js/viz/sequence-datum.js#L3-L11

Is this a case that should be dealt with or should that sequence position have been recorded differently?
E.g as "<79-79" (https://github.com/MICommunity/ComplexViewer/blob/master/src/js/viz/sequence-datum.js#L10)
Latter would make more sense because you don't really want to say it could be 90-79?

[EliotRagueneau]

I'm discussing the topics with curators to be sure of the interpretation we should come up with.
Getting back to you as soon as I have feedback 😄

[EliotRagueneau]

If it was just up to me, I think we should consider "pos": "?-79" as "pos": "0-79", but with a hatched rendering as we do when we are uncertain of the range, but let's see what curators think is the best solution for that, and if it is just needed at all.

[EliotRagueneau]

Sandra confirms it is no curation mistake, and that the best strategy to represent it would be to go from 0 to 79 with hatched display

[bmeldal]

I think "<79-79" is the correct mathematical notation but the editor wouldn't allow it. You can only use integers and ? to identify the start and end of the linked feature region. It's probably less common to be uncertain about only one end of the range but I can see where it comes from when we combine ranges from multiple experiments that are inconsistent. That experimental work for you ;-)

[colin-combe]

I think "<79-79" is the correct mathematical notation but the editor wouldn't allow it.

i think "<79-79" would describe what Eliot described - "0 to 79 with hatched display". Really, "?-79" would be hatched from start to end, but i don't think it was one of the possibilities originally given for this.

Maybe this is a mistake? and the fix is to make the editor allow "<79-79"?

[EliotRagueneau]

Sandra seemed pretty convinced that it was no mistake. The first item in the range is always lower than the second item according to the database records, so I assume the convention for curation is to put features in the "normal" reading sense. Considering that, the only possible interpretation for "?-79" is that the lower bound is not known, but the upper one is.

I agree that in theory, we could put range on opposite strands by placing the range like "a-b" where b>a for DNA, but I couldn't find any example of such features in the database, and since the main focus is proteins, it's unlikely to happen, and I would assume that by convention, curators would still put it in the "normal" direction.
I'll confirm with them.

[EliotRagueneau]

I just confirmed it with them, and at the moment, the editor doesn't even support curators to put ranges like "157-12", so we are really enforcing the direction of the feature, so no no need to introduce a new synthax for such annotations I think. Are you okay with that @colin-combe ?

[colin-combe]

Are you okay with that @colin-combe ?

yes, i'm okay with that.
So, to confirm, you'd like me to add support for "?-79"?

[EliotRagueneau]

Yes ideally, thanks a lot 😃

[colin-combe]

should be fixed by #201