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SEP V004: New Glyph Proposal Collection #8

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jakebeal opened this Issue Aug 22, 2017 · 61 comments

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jakebeal commented Aug 22, 2017

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

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:

glyph specification

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:

glyph specification

another hovering above the backbone:

glyph specification

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:

glyph specification

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:

glyph specification

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:

glyph specification

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

glyph specification

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:

glyph specification

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

glyph specificationglyph specification

Proteins can be indicated by a letter above:

glyph specification

Stop and start codons might be indicated by special symbols:

glyph specificationglyph specificationglyph specification

Edits can be indicated by changes:

glyph specificationglyph specificationglyph specificationglyph specificationglyph specificationglyph specification

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:

glyph specification

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.

glyph specification

glyph specification

Prototypical Example

Needs a good example

Notes

Potential conflict with proposed Specific Recombination Site glyph.

Non-Coding RNA

Squiggle with teeth:

glyph specification

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

glyph specification

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:

glyph specification

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:

glyph specification

glyph specification

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

glyph specification

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

glyph specification

  • A chevron with a vertical break:

glyph specification

  • A broken CDS pentagon

glyph specification

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

glyph specification

  • A CDS pentagon with a chevron break:

glyph specification

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:

glyph specification

Prototypical Example

PEST tag

Copyright

CC0
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.

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jakebeal Aug 22, 2017

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My take:
I like:

  • Aptamer: Clearly getting used in many designs. I like the first of the two versions better.
  • Non-Coding RNA: we need to distinguish functional RNAs like gRNAs from protein coding sequences, which are how they're getting represented now.
  • ORI-T: if people want it, I like how it intuitively relates to our existing origin of replication glyph
  • Protein Domain: people are already doing this in various ways, and we need a clear recommendation. I like the chevron variant best.
  • Specific Recombination Site: this glyph has already been using in a number of publications and it's clean, simple, and asymmetric.
  • Tag: nice simple, intuitive symbol for something that is used in many cases.

I dislike:

  • Codon: I think it's a lot of complexity for unclear demand.
  • Inverter: there's no clear consensus on whether this makes sense as a basic part, and the proposed symbol overlaps with recombination site.
  • Transcript Region: it's a fiddly symbol and I think Non-Coding RNA covers it well enough.

I am neutral on:

  • Homology Region
  • polyA Site
  • Non Directional Sticky End
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jakebeal commented Aug 22, 2017

My take:
I like:

  • Aptamer: Clearly getting used in many designs. I like the first of the two versions better.
  • Non-Coding RNA: we need to distinguish functional RNAs like gRNAs from protein coding sequences, which are how they're getting represented now.
  • ORI-T: if people want it, I like how it intuitively relates to our existing origin of replication glyph
  • Protein Domain: people are already doing this in various ways, and we need a clear recommendation. I like the chevron variant best.
  • Specific Recombination Site: this glyph has already been using in a number of publications and it's clean, simple, and asymmetric.
  • Tag: nice simple, intuitive symbol for something that is used in many cases.

I dislike:

  • Codon: I think it's a lot of complexity for unclear demand.
  • Inverter: there's no clear consensus on whether this makes sense as a basic part, and the proposed symbol overlaps with recombination site.
  • Transcript Region: it's a fiddly symbol and I think Non-Coding RNA covers it well enough.

I am neutral on:

  • Homology Region
  • polyA Site
  • Non Directional Sticky End
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swapnilb Aug 22, 2017

Recombinase sites have been in wide use in literature, so I would object to changing that glyph. I don't know what is meant by an inverter -- is this a device-level glyph? My impression is that our first pass (should) cover(s) biological primitive parts.

swapnilb commented Aug 22, 2017

Recombinase sites have been in wide use in literature, so I would object to changing that glyph. I don't know what is meant by an inverter -- is this a device-level glyph? My impression is that our first pass (should) cover(s) biological primitive parts.

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jakebeal Aug 22, 2017

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I'm not going to defend inverter --- it was made as a proposal, and we need to give it an up or down vote at some point. I will be voting "no" on inverter.

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jakebeal commented Aug 22, 2017

I'm not going to defend inverter --- it was made as a proposal, and we need to give it an up or down vote at some point. I will be voting "no" on inverter.

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swapnilb Aug 22, 2017

OriT was informally proposed by Angel Goni / @jakebeal / others in an SBOL Visual Thread (9/2014) to be the following:

image

I propose we consider it as a candidate glyph.

swapnilb commented Aug 22, 2017

OriT was informally proposed by Angel Goni / @jakebeal / others in an SBOL Visual Thread (9/2014) to be the following:

image

I propose we consider it as a candidate glyph.

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Thank you, Swapnil. I've added it, and like it very much as an option.

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jakebeal commented Aug 22, 2017

Thank you, Swapnil. I've added it, and like it very much as an option.

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swapnilb Aug 22, 2017

The "Tag" is somewhat confounding. The example cited is of a PEST tag, which appears to be a functional component (acts as a signal peptide for degradation). Yet, the SO term is specific to oligo tags used in identifying DNA; indeed, it's parent is an oligo.

I suggest we separate out which meaning is intended, and I also suggest we address "functional" tags (degradation, routing, fluorescence, etc) as well, if not before, identification tags, because the former have been used frequently in synthetic biology literature (e.g. Friedland et al. 2009).

swapnilb commented Aug 22, 2017

The "Tag" is somewhat confounding. The example cited is of a PEST tag, which appears to be a functional component (acts as a signal peptide for degradation). Yet, the SO term is specific to oligo tags used in identifying DNA; indeed, it's parent is an oligo.

I suggest we separate out which meaning is intended, and I also suggest we address "functional" tags (degradation, routing, fluorescence, etc) as well, if not before, identification tags, because the former have been used frequently in synthetic biology literature (e.g. Friedland et al. 2009).

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swapnilb Aug 22, 2017

Separately, my other objection to the Tag glyph is that it is not naturally scalable as may be needed to depict a sequence of varying length (whether functional, or oligo tag). It is also a simply rotated variant of another glyph, which makes us introduce two unrelated glyphs that are unnecessarily close.

swapnilb commented Aug 22, 2017

Separately, my other objection to the Tag glyph is that it is not naturally scalable as may be needed to depict a sequence of varying length (whether functional, or oligo tag). It is also a simply rotated variant of another glyph, which makes us introduce two unrelated glyphs that are unnecessarily close.

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jakebeal Aug 22, 2017

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Here is the current source for the Tag glyph proposal:

  1. The iGEM registry has many parts with "Tag" as their class, e.g. BBa_K1616026. You can see the little "gift tag" icon on the page.
  2. If you search in SynBioHub for parts with a Tag role, you can readily find all of these, and see the "cleaned up" version of the glyph that is here.
  3. Tags like these are commonly used, and it would be useful to be able to have glyphs for them, but to the best of my knowledge no other graphical convention currently exists.

You're right about the SO term being a problem, though --- if we can figure out what the right term is, that can be updated or fixed.

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jakebeal commented Aug 22, 2017

Here is the current source for the Tag glyph proposal:

  1. The iGEM registry has many parts with "Tag" as their class, e.g. BBa_K1616026. You can see the little "gift tag" icon on the page.
  2. If you search in SynBioHub for parts with a Tag role, you can readily find all of these, and see the "cleaned up" version of the glyph that is here.
  3. Tags like these are commonly used, and it would be useful to be able to have glyphs for them, but to the best of my knowledge no other graphical convention currently exists.

You're right about the SO term being a problem, though --- if we can figure out what the right term is, that can be updated or fixed.

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mgaldzic commented Aug 23, 2017

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swapnilb Aug 23, 2017

Is anyone more familiar with http://obofoundry.org/ontology/pr.html -- has terms closer in meaning to some of the "functional" tags. (Some of the links don't appear to work.)

swapnilb commented Aug 23, 2017

Is anyone more familiar with http://obofoundry.org/ontology/pr.html -- has terms closer in meaning to some of the "functional" tags. (Some of the links don't appear to work.)

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chofski Aug 25, 2017

Here are my views:

  • Aptamer: I prefer the first variant that I've seen used a lot.
  • Codons: I find all of these very confusing and specific. Personally, it seems like a level below what is useful as a standard design language (and doesn't stop people annotating SBOLv designs with this information as they see fit).
  • Homology: fine by me and would be nice to have a general symbol to highlight key areas of homology.
  • Inverter: Have no idea what this is actually representing and would remove.
  • Non-coding RNA: I like the squiggle with teeth is possible (I think this was discussed previously).
  • Origin of Transfer: Prefer the circle with arrow. I find spirals difficult to draw.
    All other ones I'm happy with what is proposed.

chofski commented Aug 25, 2017

Here are my views:

  • Aptamer: I prefer the first variant that I've seen used a lot.
  • Codons: I find all of these very confusing and specific. Personally, it seems like a level below what is useful as a standard design language (and doesn't stop people annotating SBOLv designs with this information as they see fit).
  • Homology: fine by me and would be nice to have a general symbol to highlight key areas of homology.
  • Inverter: Have no idea what this is actually representing and would remove.
  • Non-coding RNA: I like the squiggle with teeth is possible (I think this was discussed previously).
  • Origin of Transfer: Prefer the circle with arrow. I find spirals difficult to draw.
    All other ones I'm happy with what is proposed.
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swapnilb Aug 25, 2017

Regarding the Protein Domain glyph:
I am a little confused.

  1. I suspect that this glyph would necessarily have to be composable with CDS glyph(s), without confounding the meaning of the CDS glyph.
  2. Protein Domains, I presume, can be integrated into any protein, as per classic synbio paradigm.
  3. Now, take any of the 5 out of the 6 proposed glyphs. They all have arrowheads.
  4. So if we were to represent domain X engineered into the middle of a CDS coding for protein Y, then we would have a "composite glyph" that looked like

image

where the red glyph (assume it is one of the 5 proposed above) is the engineered domain. This at best, can be a bit confusing, because of the extra arrowhead. How would a CDS encoding a fusion proteinor a multi-CDS construct be denoted, without confounding it with Protein Domains?

FWIW, pigeon has allowed for fusion CDSes to be denoted as follows, and it has seen quite a bit of use (judging from several folks who signed up to ask for it, out of the blue):

image

swapnilb commented Aug 25, 2017

Regarding the Protein Domain glyph:
I am a little confused.

  1. I suspect that this glyph would necessarily have to be composable with CDS glyph(s), without confounding the meaning of the CDS glyph.
  2. Protein Domains, I presume, can be integrated into any protein, as per classic synbio paradigm.
  3. Now, take any of the 5 out of the 6 proposed glyphs. They all have arrowheads.
  4. So if we were to represent domain X engineered into the middle of a CDS coding for protein Y, then we would have a "composite glyph" that looked like

image

where the red glyph (assume it is one of the 5 proposed above) is the engineered domain. This at best, can be a bit confusing, because of the extra arrowhead. How would a CDS encoding a fusion proteinor a multi-CDS construct be denoted, without confounding it with Protein Domains?

FWIW, pigeon has allowed for fusion CDSes to be denoted as follows, and it has seen quite a bit of use (judging from several folks who signed up to ask for it, out of the blue):

image

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jakebeal Aug 25, 2017

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@swapnilb I agree that most of the proposed glyphs for Protein Domain don't compose nicely. The two that do are:

  • "User Defined" rectangle: this is effectively equivalent to your current fusion CDS model, but reuses rectangles, thus giving potential for confusion.
  • chevron: this works just the same way, except that the "internal" line is bent forward rather than being straight up and down. This provides the same functionality, but removes the ambiguity.

This is why I like chevron best of the options. We could further clarify the composition as a note, saying something like "when a Protein Domain is indicated within a CDS, 'internal' boundaries use the chevron, while boundaries at the extremes of the CDS follow the convention of the CDS"

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jakebeal commented Aug 25, 2017

@swapnilb I agree that most of the proposed glyphs for Protein Domain don't compose nicely. The two that do are:

  • "User Defined" rectangle: this is effectively equivalent to your current fusion CDS model, but reuses rectangles, thus giving potential for confusion.
  • chevron: this works just the same way, except that the "internal" line is bent forward rather than being straight up and down. This provides the same functionality, but removes the ambiguity.

This is why I like chevron best of the options. We could further clarify the composition as a note, saying something like "when a Protein Domain is indicated within a CDS, 'internal' boundaries use the chevron, while boundaries at the extremes of the CDS follow the convention of the CDS"

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swapnilb Aug 25, 2017

@jakebeal Agree with almost everything in your latest comment, except one point:

One problem with the chevron is that if you have overlapping domains, not an entirely rare use case, then if you overlap two chevrons, you can get an unintended number of chevrons. This is because of the identical geometry of the pair of lines at the start and end of the chevron. If we could fix this, then a chevron glyph for PD could work well.

swapnilb commented Aug 25, 2017

@jakebeal Agree with almost everything in your latest comment, except one point:

One problem with the chevron is that if you have overlapping domains, not an entirely rare use case, then if you overlap two chevrons, you can get an unintended number of chevrons. This is because of the identical geometry of the pair of lines at the start and end of the chevron. If we could fix this, then a chevron glyph for PD could work well.

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I believe we've got lots of good options for distinguishing overlapping domains. One is simply to use fills that indicate the overlap:

f3wkr

One can also do it way vertical separation, textual annotations, etc. The preference will likely depend on the circumstance.

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jakebeal commented Aug 25, 2017

I believe we've got lots of good options for distinguishing overlapping domains. One is simply to use fills that indicate the overlap:

f3wkr

One can also do it way vertical separation, textual annotations, etc. The preference will likely depend on the circumstance.

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swapnilb Aug 25, 2017

It is not clear: my use case is that in a drawing such as yours, domain red and domain blue overlap in the grey CDS. That is, domain blue would be codons b_i to b_j and red would be r_i to r_j, where b_i < r _i < b_j < r_j. In this case, we would get an unintended purple chevron, as you have shown. It is not immediately clear from your picture, that the purple chevron is NOT a third PD. In fact, it is very nicely suggestive of the purple chevron being a third PD. This is undesirable in designing a glyph.

swapnilb commented Aug 25, 2017

It is not clear: my use case is that in a drawing such as yours, domain red and domain blue overlap in the grey CDS. That is, domain blue would be codons b_i to b_j and red would be r_i to r_j, where b_i < r _i < b_j < r_j. In this case, we would get an unintended purple chevron, as you have shown. It is not immediately clear from your picture, that the purple chevron is NOT a third PD. In fact, it is very nicely suggestive of the purple chevron being a third PD. This is undesirable in designing a glyph.

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So spread out the hatching a bit so it's less ambiguous, or use outlines instead, or text... my point is that I find this to be solvable with the tools already at hand.

chevronsa

chevronsb

chevronsc

chevronsd

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jakebeal commented Aug 25, 2017

So spread out the hatching a bit so it's less ambiguous, or use outlines instead, or text... my point is that I find this to be solvable with the tools already at hand.

chevronsa

chevronsb

chevronsc

chevronsd

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I have updated the SEP based on the current state of discussion. Here is what I am currently seeing:

Symbols with apparent consensus in favor of a specific glyph:

  • Aptamer: cartoon secondary structure
  • ORI-T: circle-with-arrow
  • Specific Recombination Site: triangle

Symbols with apparent consensus, but multiple glyph options yet to be resolved:

  • Non-Coding RNA / Transcript Region: which option, or should we consider yet another?
  • Protein Domain: chevron or "User Defined" rectangle?

Symbols without a clear consensus:

  • Tag: SO term problem, are we OK with the glyph?
  • Homology Region: needs more voices in favor or against
  • polyA Site: needs more voices in favor or against
  • Non Directional Sticky End: needs more voices in favor or against

Symbols with apparent consensus against:

  • Codon: high complexity, low demand
  • Inverter: no clear meaning, no demand, conflict with Specific Recombination Site
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jakebeal commented Aug 26, 2017

I have updated the SEP based on the current state of discussion. Here is what I am currently seeing:

Symbols with apparent consensus in favor of a specific glyph:

  • Aptamer: cartoon secondary structure
  • ORI-T: circle-with-arrow
  • Specific Recombination Site: triangle

Symbols with apparent consensus, but multiple glyph options yet to be resolved:

  • Non-Coding RNA / Transcript Region: which option, or should we consider yet another?
  • Protein Domain: chevron or "User Defined" rectangle?

Symbols without a clear consensus:

  • Tag: SO term problem, are we OK with the glyph?
  • Homology Region: needs more voices in favor or against
  • polyA Site: needs more voices in favor or against
  • Non Directional Sticky End: needs more voices in favor or against

Symbols with apparent consensus against:

  • Codon: high complexity, low demand
  • Inverter: no clear meaning, no demand, conflict with Specific Recombination Site
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@chofski With respect to ncRNA, are you thinking something like this?

glyph specification

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jakebeal commented Aug 26, 2017

@chofski With respect to ncRNA, are you thinking something like this?

glyph specification

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chofski Aug 26, 2017

Yes, precisely. Or slight variations on it, e.g., where the "teeth" are perpendicular to the backbone and not all parallel.

chofski commented Aug 26, 2017

Yes, precisely. Or slight variations on it, e.g., where the "teeth" are perpendicular to the backbone and not all parallel.

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@chofski Would you be willing to say what you prefer about the "teeth" version over the "no teeth" version? Personally, I prefer the "no teeth" version because it is simpler to draw and matches the RNA symbols that I have seen in a number of scientific papers (e.g., http://www.nature.com/nbt/journal/v33/n8/abs/nbt.3301.html)

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jakebeal commented Aug 26, 2017

@chofski Would you be willing to say what you prefer about the "teeth" version over the "no teeth" version? Personally, I prefer the "no teeth" version because it is simpler to draw and matches the RNA symbols that I have seen in a number of scientific papers (e.g., http://www.nature.com/nbt/journal/v33/n8/abs/nbt.3301.html)

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chofski Aug 26, 2017

Yes, but it is a minor preference. I'd be happy with either to be adopted.

chofski commented Aug 26, 2017

Yes, but it is a minor preference. I'd be happy with either to be adopted.

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Thank you for the clarifications. I've added the "teeth" version to the options under consideration, and we'll see how the conversation continues to develop.

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jakebeal commented Aug 26, 2017

Thank you for the clarifications. I've added the "teeth" version to the options under consideration, and we'll see how the conversation continues to develop.

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graik Aug 27, 2017

The issue with the protein domain suggestions so far is that they are very unlike anything that is actually informally being used in the field today. The most common symbols being used currently are:

  • simple rectangle (undefined in SBOL, so presumably that's not a good symbol)
  • Elipse
  • rounded rectangle
    I would therefore like to formally suggest the latter as the recommended symbol for protein domains:

sep004_protein_domain_suggestion

I would further suggest that protein features are recommended to be placed above (or below) the encompassing CDS symbol, possibly with an extra baseline that is symbolizing the protein.

graik commented Aug 27, 2017

The issue with the protein domain suggestions so far is that they are very unlike anything that is actually informally being used in the field today. The most common symbols being used currently are:

  • simple rectangle (undefined in SBOL, so presumably that's not a good symbol)
  • Elipse
  • rounded rectangle
    I would therefore like to formally suggest the latter as the recommended symbol for protein domains:

sep004_protein_domain_suggestion

I would further suggest that protein features are recommended to be placed above (or below) the encompassing CDS symbol, possibly with an extra baseline that is symbolizing the protein.

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swapnilb Aug 27, 2017

@chofski @jakebeal I highly prefer the non-teeth version for RNA. Teeth has way too high stroke complexity.

Also, if I understand correctly, we should be careful to call it "DNA encoding ncRNA" -- in that this glyph cannot be used to depict the RNA transcribed. (Or if it can, then that should be mentioned in the spec.) I also prefer the boxed variant for ncRNA since it clearly shows it as being part of the DNA.

As to chevron -- I understand that the problem can be solved, but I don't support adding a known confusion into the spec. The overlap problem needs to be dealt with at some point, and it is best if we don't make it worse.

swapnilb commented Aug 27, 2017

@chofski @jakebeal I highly prefer the non-teeth version for RNA. Teeth has way too high stroke complexity.

Also, if I understand correctly, we should be careful to call it "DNA encoding ncRNA" -- in that this glyph cannot be used to depict the RNA transcribed. (Or if it can, then that should be mentioned in the spec.) I also prefer the boxed variant for ncRNA since it clearly shows it as being part of the DNA.

As to chevron -- I understand that the problem can be solved, but I don't support adding a known confusion into the spec. The overlap problem needs to be dealt with at some point, and it is best if we don't make it worse.

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swapnilb Aug 27, 2017

@graik I concur that we need to develop a standard way to describe overlapping features. I agree, the PD would be better illustrated if it could be aligned beside the CDS.

swapnilb commented Aug 27, 2017

@graik I concur that we need to develop a standard way to describe overlapping features. I agree, the PD would be better illustrated if it could be aligned beside the CDS.

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swapnilb Aug 27, 2017

@jakebeal please note this too:

Tag: I object to the current glyph because:

  • it is a rotated version of the CDS. No compelling reason it should be.
  • It is not naturally scalable in the X direction.
  • Minor: cartoon price tags have a hole at the pointy end.

swapnilb commented Aug 27, 2017

@jakebeal please note this too:

Tag: I object to the current glyph because:

  • it is a rotated version of the CDS. No compelling reason it should be.
  • It is not naturally scalable in the X direction.
  • Minor: cartoon price tags have a hole at the pointy end.
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Also, if I understand correctly, we should be careful to call it "DNA encoding ncRNA" -- in that this glyph cannot be used to depict the RNA transcribed.

@swapnilb I believe the associated SO term is clear: "SO:0001263: Non-Coding RNA Gene", so I've changed the glyph name in the SEP to be exactly that.

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jakebeal commented Aug 27, 2017

Also, if I understand correctly, we should be careful to call it "DNA encoding ncRNA" -- in that this glyph cannot be used to depict the RNA transcribed.

@swapnilb I believe the associated SO term is clear: "SO:0001263: Non-Coding RNA Gene", so I've changed the glyph name in the SEP to be exactly that.

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cjmyers Sep 14, 2017

I think we might want to see if we can get the SO folks to add a parent to the RNA coding regions of the DNA that are not mRNAs. In other words a child of 834 that is a parent to all but 836.

cjmyers commented Sep 14, 2017

I think we might want to see if we can get the SO folks to add a parent to the RNA coding regions of the DNA that are not mRNAs. In other words a child of 834 that is a parent to all but 836.

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That would still be problematic because 836 contains things like "riboswitch" and "RNA thermometer" that are functional RNA rather than protein coding RNA.

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jakebeal commented Sep 14, 2017

That would still be problematic because 836 contains things like "riboswitch" and "RNA thermometer" that are functional RNA rather than protein coding RNA.

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cjmyers Sep 14, 2017

These though are still part of the mRNA to regulate its translation into a protein though? I thought the distinction we are wanting is a glyph that indicates that the region codes for protein or does not code for protein. My understanding is that mRNA codes for protein, and the other RNA options here do not, even if parts of the mRNA region are there only for regulation of translation.

cjmyers commented Sep 14, 2017

These though are still part of the mRNA to regulate its translation into a protein though? I thought the distinction we are wanting is a glyph that indicates that the region codes for protein or does not code for protein. My understanding is that mRNA codes for protein, and the other RNA options here do not, even if parts of the mRNA region are there only for regulation of translation.

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I believe that things like riboswitches might be used to regulate other functional RNA as well, by modulating its stability. I am not certain, but certainly wouldn't count on artificial systems remaining isolated thus.

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jakebeal commented Sep 14, 2017

I believe that things like riboswitches might be used to regulate other functional RNA as well, by modulating its stability. I am not certain, but certainly wouldn't count on artificial systems remaining isolated thus.

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For now, I have merged the two, giving both SO terms.

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jakebeal commented Sep 14, 2017

For now, I have merged the two, giving both SO terms.

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Returning to the question of protein domains: I would like to remove the "rectangle" option. My reasons are:

  1. It is redundant with the use of rectangle for Unspecified. Thus, if we want "rectangle", we should just not assign a glyph.
  2. At the same time, it will conflict with the use of rectangle in Composite and (likely) No Glyph Assigned

@swapnilb @graik @cjmyers Would you be OK with this?

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jakebeal commented Sep 17, 2017

Returning to the question of protein domains: I would like to remove the "rectangle" option. My reasons are:

  1. It is redundant with the use of rectangle for Unspecified. Thus, if we want "rectangle", we should just not assign a glyph.
  2. At the same time, it will conflict with the use of rectangle in Composite and (likely) No Glyph Assigned

@swapnilb @graik @cjmyers Would you be OK with this?

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I'd also like to pick just one of the three ncRNA options, if we can. Would people be OK with the recommended vote being: "pick one" rather than "do you like all three as alternatives"? And can we eliminate any before voting?

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jakebeal commented Sep 17, 2017

I'd also like to pick just one of the three ncRNA options, if we can. Would people be OK with the recommended vote being: "pick one" rather than "do you like all three as alternatives"? And can we eliminate any before voting?

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On ncRNA, a bit of searching around the literature online finds that the main ways of diagramming ncRNA at present are:

  • "single strand wiggles"
  • unspecified rectangles
  • complex shape diagrams

I thus propose to remove the "peeling teeth" ncRNA from consideration, then put "wiggle" vs. "box-wiggle" to a vote, since I know that I strongly prefer "wiggle" and @swapnilb has stated that he prefers "box-wiggle".

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jakebeal commented Sep 17, 2017

On ncRNA, a bit of searching around the literature online finds that the main ways of diagramming ncRNA at present are:

  • "single strand wiggles"
  • unspecified rectangles
  • complex shape diagrams

I thus propose to remove the "peeling teeth" ncRNA from consideration, then put "wiggle" vs. "box-wiggle" to a vote, since I know that I strongly prefer "wiggle" and @swapnilb has stated that he prefers "box-wiggle".

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swapnilb Sep 17, 2017

I strongly prefer "box-wiggle." To reiterate: this is the DNA encoding some ncRNA. So I like that it is attached to the backbone and NOT hovering.

I think we should punt on protein domains. It requires more careful design. So I am OK with removing the rectangle option at the very least.

For the protein domain chevron, I am still NOT OK with it. It's known to not be, and by design, is not a good glyph. Therefore, I propose that we have another symbol such that none of its X-directional overlapping translations forms an unintended glyph. Any glyph that smoothly varies in the X/-X direction would do the job, and would improve the visualization of overlapping domains, which is likely a common use case.

swapnilb commented Sep 17, 2017

I strongly prefer "box-wiggle." To reiterate: this is the DNA encoding some ncRNA. So I like that it is attached to the backbone and NOT hovering.

I think we should punt on protein domains. It requires more careful design. So I am OK with removing the rectangle option at the very least.

For the protein domain chevron, I am still NOT OK with it. It's known to not be, and by design, is not a good glyph. Therefore, I propose that we have another symbol such that none of its X-directional overlapping translations forms an unintended glyph. Any glyph that smoothly varies in the X/-X direction would do the job, and would improve the visualization of overlapping domains, which is likely a common use case.

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@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.

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jakebeal commented Sep 18, 2017

@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.

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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:

glyph specification
glyph specification
glyph specification

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

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jakebeal commented Sep 18, 2017

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:

glyph specification
glyph specification
glyph specification

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

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swapnilb Sep 18, 2017

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.)

swapnilb commented Sep 18, 2017

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.)

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@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.

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jakebeal commented Sep 18, 2017

@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.

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swapnilb Sep 18, 2017

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

swapnilb commented Sep 18, 2017

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

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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.

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jakebeal commented Sep 18, 2017

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.

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bbartley Sep 18, 2017

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

bbartley commented Sep 18, 2017

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

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@bbartley SO reference?

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jakebeal commented Sep 18, 2017

@bbartley SO reference?

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bbartley Sep 18, 2017

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

bbartley commented Sep 18, 2017

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

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

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jakebeal commented Sep 18, 2017

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

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