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update per discussion

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jakebeal
jakebeal committed Jun 10, 2019
1 parent 0b16ece commit 994748caed007d4073ff51785eb8fd6fa21b1310
Showing with 14 additions and 14 deletions.
  1. +14 −14 SEPs/SEP_V017.md
@@ -37,10 +37,9 @@ We thus propose the following changes:
Macromolecule is either left unchanged or has the "shmoo" deprecated.

### Alternatives that must be voted on:
1. Should Macromolecule a) have rounded-rectangle become RECOMMENDED, leaving "shmoo" as an alternative, or c) have rounded rectangle become RECOMMENDED and deprecate "shmoo".
1. Should Macromolecule a) have rounded-rectangle become RECOMMENDED, leaving "shmoo" as an alternative, or b) have rounded rectangle become RECOMMENDED and deprecate "shmoo" (i.e., mark it for future removal).
2. Should we adopt the "pill" Protein glyph, or just represent proteins using the Macromolecule rounded-rectangle?
3. If Protein is adopted, should it include an alternate with lines sticking from its ends?
4. Should the recommended glyph for Simple Chemical be the hexagon or the small circle?
3. Should the RECOMMENDED glyph for Simple Chemical be (a) stretchable hexagon or (b) small circle?

## 2. Specification <a name="specification"></a>

@@ -56,10 +55,6 @@ The protein glyph is a "pill" shape with a rectangular body and rounded ends, re

![glyph specification](https://raw.githubusercontent.com/SynBioDex/SBOL-visual/d792cc5/Glyphs/FunctionalComponents/protein/protein-specification.png)

Potential alternate: a "pill" shape with lines extending from its ends.

![glyph specification](https://user-images.githubusercontent.com/1862877/58933854-41698780-8771-11e9-8eed-538147bfbf2d.png)


#### Prototypical Example

@@ -108,19 +103,19 @@ Alternate BioPAX definition: Small Molecule: http://www.biopax.org/release/biopa

### Complex

Examples are updated to match new glyphs for this SEP:
Examples will be updated to match new glyphs for this SEP. One set of possible updates:

* Protein (as macromolecule) bound with small molecule:
* Protein bound with small molecule (stretchable hexagon version):

![glyph specification](https://raw.githubusercontent.com/SynBioDex/SBOL-visual/21b2dec/Glyphs/FunctionalComponents/complex/complex-ps-specification.png)
![glyph specification](https://raw.githubusercontent.com/SynBioDex/SBOL-visual/7371b94/Glyphs/FunctionalComponents/complex/complex-ps-specification.png)

* Protein (as macromolecule) bound with alternative small molecule:
* Protein (as macromolecule) bound with small molecule (small circle version):

![glyph specification](https://raw.githubusercontent.com/SynBioDex/SBOL-visual/21b2dec/Glyphs/FunctionalComponents/complex/complex-ps-alt-specification.png)

* Protein (as macromolecule) bound with RNA:
* Protein bound with RNA:

![glyph specification](https://raw.githubusercontent.com/SynBioDex/SBOL-visual/21b2dec/Glyphs/FunctionalComponents/complex/complex-pr-specification.png)
![glyph specification](https://raw.githubusercontent.com/SynBioDex/SBOL-visual/7371b94/Glyphs/FunctionalComponents/complex/complex-pr-specification.png)

* Two proteins bound together:

@@ -134,7 +129,7 @@ Examples are updated to match new glyphs for this SEP:

## 4. Backwards Compatibility <a name='compatibility'></a>

The "shmoo" Macromolecule glyph is being retained to support backward compatibility.
The "shmoo" Macromolecule glyph is being retained to support backward compatibility. It may or may not be schedule for deletion at a future date, depending on the outcome of the deprecation vote.

Of greater concern is the fact that "pill" (or "stadium") has been used to represent simple chemicals in published diagrams that will now be invalid.

@@ -151,6 +146,11 @@ Strong concerns were raised regarding the potential confusion between ellipse, p

Backwards compatibility and compatibility with SBGN are also issues, but the consensus seems to have been that compatibility with "pill" images of proteins, including in the pending protein language, is more important. SBGN compatibility is still maintained, however, via Macromolecule and the circle variant of Simple Chemical.

A potential alternate glyph for protein is currently being deferred: a "pill" shape with lines extending from its ends.

![glyph specification](https://user-images.githubusercontent.com/1862877/58933854-41698780-8771-11e9-8eed-538147bfbf2d.png)



## Copyright <a name='copyright'></a>

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