SEP V012: Stop Codons

[chofski]

This SEP proposes an explicit way of representing stop codons (useful if this feature needs to be highlighted). I have included two variants based on discussions on the mailing list.

Full proposal is at: https://github.com/SynBioDex/SBOL-visual/blob/develop/SEPs/SEP_V012.md

[jakebeal]

Thank you, Tom.

Two questions:

1. Are you recommending that both of these glyphs by adopted, or are you looking for the community to come to consensus on one of the two? Unless there is a strong reason to go for both, I would suggest we aim to come to consensus on one of the two, because it is generally preferable to limit the number of approved variants (increased coherence, reserved alternatives).
2. In the prior discussion, my impression had been that the cross went all the way to the corners, and I personally prefer that to the disconnected cross version that is now being shown. Can we add that as a potential option as well, or do you have a reason to recommend against it?

[jakebeal]

On a side note: per GitFlow development protocol (as noted in the top-level README), while the SEP should be on the develop branch the new glyphs should be on a feature branch, not develop. I have made that adjustment, putting the stop codon draft glyphs into https://github.com/SynBioDex/SBOL-visual/tree/feature/stop-codon and updating the links in the SEP.

[chofski]

OK, I'll make the revision. I'd suggest the cross glyph as it is simpler and will extend the ends to reach the box. Apologies about not following branch conventions... I'm new to the GitFlow approach.

[jakebeal]

No criticism, just gentle adjustment. :-)

I like the cross version too; let's see if any voices get raised for the alternatives.

[JS3xton]

I suppose I will jump in for the alternative. The cross glyph evokes a Cleavage Site stem-top glyph to me (the only difference being the bounding box as far as I can tell). As such, I prefer the asterisk over the cross. I would also lobby for inclusion of a symmetric 8-pointed asterisk alternative, because that's how I usually draw asterisks by hand.

Also, is there a good reason to employ the DNA stem over the RNA stem for this glyph?

[chofski]

Very good points by all. It makes sense to have it for both DNA and RNA as they are encoded in these substrates. I don't actually have a preference whether it is a cross or asterisk – @jakebeal are you happy to go with the asterisk, or are you still in favour of the cross?

[jakebeal]

On cross vs. asterisk --- I think @JS3xton makes a good point, and I am happy to go for the asterisk. I will also note that if we specify that the shape is an asterisk, then we need note consider 5-pointed vs. 6-pointed vs. 8-pointed --- all are "font level style differences" covered by the definition.

Regarding DNA vs. RNA stem: again @JS3xton brings up a good point. If we follow the general semantics of stem-top glyphs, then RNA stem would make sense as stop codon. DNA stem would then mean Transcription End Site (SO:0000616). No protein stem would be defined at this time.

[jakebeal]

@chofski Since we seem to have reached a point of reasonable consensus, can you please update the SEP accordingly? I'd like to then get both this and SEP V011 moved for a vote together.

[chofski]

I will make the updates. My only comment is that I'm not convinced that site should be defined for the DNA stem as the SEP is concerned solely with stop codons and not related to transcription.

[jakebeal]

I was suggesting that we expand to include transcription end site as well as stop codons.
How about including that as an option for people to discuss and vote on?
I'll be fine if people decide that's a bridge too far and vote not to do transcription, but I think it's a consistent generalization and would like to see if others agree in the wider community.

[chofski]

I've updated the SEP and after checking the biopolymer location symbols, updated them to be compatible. I've also changed the SEP from stop codons, to end points of transcription and translation, which I feel better captures the actual meaning.