SEP V004: New Glyph Proposal Collection

[jakebeal]

SEP V004: New Glyph Collection

SEP
Authors	Jacob Beal (jakebeal@ieee.org)
Editor
Type	Specification
SBOL Visual Version	1.1
Status	Draft
Created	22-Aug-2017
Last modified	18-Sep-2017

Abstract

A number of new glyphs have been proposed over the past few years, and we need to put them to an up-or-down vote.

There are twelve proposals currently pending: Aptamer, Codon, Homology Region, Inverter, Non-Coding RNA, ORI-T, polyA Site, Protein Domain, Specific Recombination Site, Non Directional Sticky End, Tag, Transcript Region

Table of Contents

• 1. Rationale
• 2. Specification
• 3. Example or Use Case
• 4. Backwards Compatibility
• 5. Discussion
• References
• Copyright

1. Rationale

Each glyph detailed below in its specification has been provided with an individual rationale for that glyph. Examples are also embedded within each proposal.

2. Specification

Aptamer

Associated SO term(s)

SO:0000031: Aptamer

Recommended Glyph and Alternates

The proposed aptamer glyph is a cartoon diagram of nucleic acid secondary structure like that found in aptamers:

Prototypical Example

theophylline aptamer

Non-Coding RNA Gene

Associated SO term(s)

SO:0001263: Non-Coding RNA Gene SO:0000834: Mature Transcript Region

Recommended Glyph and Alternates

Two of the proposed non-coding RNA glyphs are both single-stranded RNA "wiggles," one on top of a box:

another hovering above the backbone:

One or the other of these should be chosen, but not both.

Prototypical Example

gRNA

ORI-T

Associated SO term(s)

SO:0000724: Origin of Transfer

Recommended Glyph and Alternates

The origin of transfer glyph is circular like Origin of Replication, but also includes an outbound arrow:

Prototypical Example

oriT

Notes

The recommended backbone location of Origin of Replication is not yet fixed; the backbone location of this glyph is intended to match Origin of Replication, so it that is recommended to become below the glyph, this backbone location will shift as well.

polyA site

Associated SO term(s)

SO:0000553: polyA Site

Recommended Glyph and Alternates

The polyA site glyph is a sequence of As sitting atop the backbone:

Prototypical Example

polyA tail on mammalian coding sequence

Specific Recombination Site

Associated SO term(s)

SO:0000299: Specific Recombination Site

Recommended Glyph and Alternates

The specific recombination site glyph is a triangle, centered on the backbone, as has appeared in a number of recombinase circuit papers:

Prototypical Example

flippase recognition target (FRT) site

Notes

Potential conflict with proposed Inverter glyph.

3. Examples

See examples in individual glyph proposals.

4. Backwards Compatibility

All proposals are for new glyphs that do not conflict with existing glyphs. Note that two proposals (Inverter and Recombinase Site) do conflict with one another.

5. Discussion

The following proposed options have been considered, but do not have strong support and are thus being removed from consideration unless they pick up significant advocacy. They may be revisited in the future.

Aptamer

Codon

Associated SO term(s)

SO:0000360: Codon

SO:0000318: Start Codon

SO:0000319: Stop Codon

Recommended Glyph and Alternates

The proposed aptamer glyphs are two versions of a cartoon diagram of nucleic acid secondary structure like that found in aptamers:

Nucleotides can be indicated with colors or letters in the boxes:

Proteins can be indicated by a letter above:

Stop and start codons might be indicated by special symbols:

Edits can be indicated by changes:

Prototypical Example

UGA stop codon

Notes

If accepted, there will need to be additional work done to elaborate the full specification.

Homology Region

Associated SO term(s)

SO:0000853

Recommended Glyph and Alternates

The homology region glyph is a stretched hexagon hovering above the backbone:

Prototypical Example

Needs a good example

Inverter

Associated SO term(s)

No SO term currently exists

Recommended Glyph and Alternates

The inverter glyph is a triangle, echoing the buffer glyph from electronics. It might be either above or on the backbone.

Prototypical Example

Needs a good example

Notes

Potential conflict with proposed Specific Recombination Site glyph.

Non-Coding RNA

Squiggle with teeth:

Peeling comb suggesting an RNA sequence partially attached to the backbone:

Non Directional Sticky End

Associated SO term(s)

SO:0001692 (unspecified direction)

Recommended Glyph and Alternates

A sticky restriction site of unspecified direction is an angled set of cuts:

Prototypical Example

EcoRI restriction site.

ORI-T

Spirals outward toward a new destination rather than being a closed circle. Two slightly different variants of spiral are proposed for consideration:

Protein Domain

Associated SO term(s)

SO:0000417 Polypeptide Domain

Recommended Glyph and Alternates

A number of proposals have been made for Protein Domain glyphs. These are:

• A chevron, which composes nicely with the standard CDS pentagon

• A plain rectangle (the same as user defined):

• A chevron with a vertical break:

• A broken CDS pentagon

• A broken arrow (i.e., broken alternate CDS)

• A CDS pentagon with a chevron break:

Prototypical Example

VP64 activation domain

Notes

Protein domain should have the same recommended vertical position as CDS, but CDS does not have a recommended vertical position yet, so these proposals do not either.

Tag

Associated SO term(s)

SO:0000324: Tag

Recommended Glyph and Alternates

The tag glyph is a diagonal rectangle with clipped corners, reminiscent of a stereotypical paper gift tag:

Prototypical Example

PEST tag

Copyright

To the extent possible under law, SBOL developers has waived all copyright and related or neighboring rights to SEP V004. This work is published from: United States.

[jakebeal]

@cjmyers Do you have any problem with deferring on protein domain for now? I think @swapnilb makes a good case for deferring, and I would be OK with doing so --- I don't think it's a burning need, and in the mean time we can still use rectangles.

[cjmyers]

The iGEM dataset does have protein domains, so it would be nice to get this resolved. Also, I would be against reverting to rectangle assuming the new No Assigned Glyph passes. It should shift to "[ protein domain ]” instead.

@swapnil can you put forth a concrete alternative for protein domain that satisfies your concerns?

On Sep 17, 2017, at 11:23 PM, Jacob Beal notifications@github.com wrote:

@cjmyers https://github.com/cjmyers Do you have any problem with deferring on protein domain for now? I think @swapnilb https://github.com/swapnilb makes a good case for deferring, and I would be OK with doing so --- I don't think it's a burning need, and in the mean time we can still use rectangles.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/SynBioDex/SBOLv-realizations/issues/8#issuecomment-330131503, or mute the thread https://github.com/notifications/unsubscribe-auth/ADWD91iRX9-VkhXQwFwaryk0kmmpFxzeks5sjf5EgaJpZM4O_B9B.

[jakebeal]

I made a couple of other variants of the "wiggle-box" ncRNA that have what I find to be a prettier wiggle. They're not actually intended to be different alternative glyphs, just different stylings in search of one that best presents the "wiggle-box" option. Here are the three current stylings:

@swapnilb Which of these stylings do you like the best?

[swapnilb]

I don't have a preference among these, because I consider them in the same equivalence class. Indeed, I think we should allow any reasonable "wiggle," including a pointy "resistor" style wiggle.

(Side note: If we are pedantic about glyph elements, we may turn away people without very precise drawing skills. We should design for everyone. So our glyphs need to have a good "noise margin" around them. I consider the wiggle type to fall in that margin.)

[jakebeal]

@swapnilb OK, I'm picking the one I find "prettiest," and we'll see which way the votes go. I do think that "sawtooth" is different from "wiggle" --- or at least it certainly will be if we end up choosing that option on SEP V007.

I've also moved "protein domain" into the "not moving forward" section for now. They'll end up getting rendered as No Glyph Assigned (per outcome of SEP V006) unless a better suggestion gets made and adopted.

[swapnilb]

OK -- though we should reconsider accepting glyphs within a very small edit distance from another glyph -- wiggle and saw tooth are a good example.

[jakebeal]

Understood. It may be worth noting that the difference is quite similar to inductor vs. resistor in electronic symbols --- whether that argues for or against, though, is a matter of opinion.

[bbartley]

Just a quick observation. Homology region DOES have an associated SO term, sort of: "homologous_to"

[jakebeal]

@bbartley SO reference?

[bbartley]

Rather than homologous_to (which is in the Relationship branch of SO), there is also SO:0000853 (homologous_region) which is a child of SO:0000857 (homologous). These latter are probably more appropriate terms.

See http://www.sequenceontology.org/browser/current_svn/term/SO:0000853

[jakebeal]

Great: marked it with SO:0000853, for future reference.

[jakebeal]

Accepted and integrated, and thus closed per SBOL procedure in updated SEP 001.