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SEP V009: Engineered Region vs. Composite #16

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jakebeal opened this Issue Oct 7, 2017 · 4 comments

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jakebeal commented Oct 7, 2017

SEP V009: Engineered Region vs. Composite

SEP
Authors Jacob Beal (jakebeal@ieee.org), Chris Myers, John Sexton
Editor
Type Specification
SBOL Visual Version 1.1
Status Draft
Created 7-Oct-2017
Last modified Never

Abstract

This SEP proposes to split Engineered Region from Composite.

1. Rationale

The Engineered Region SO term (SO:0000804) currently assigned to the Composite glyph does not actually describe composite parts: some engineered regions are not meaningfully composites, and some multi-element composites are better described by terms not covered by Engineered Region (e.g., a double terminator, or an evolved gene cluster).

This SEP thus proposes to split the two terms, giving Engineered Region the Rectangle glyph. The rectangle will also be eventually removed from Unspecified.

2. Specification

Engineered Region

Associated SO term: SO:0000804 Engineered Region

Glyph: Rectangle

Composite

The Composite glyph will no longer have a specific SO term. Instead, there will be the following note:

Composite does not have an associated SO term, as it merely links a base glyph (with its own SO term) to a sub-diagram (comprising glyphs with their own associated SO terms).

The Rectangle glyph will no longer be an alternative for Composite.

Unspecified

The Rectangle alternative will be deprecated and given RECOMMEND NOT status for Unspecified in SBOL Visual 1.1, then removed entirely in SBOL Visual 2.0.

3. Examples

Engineered Region might represent a DNA component containing both a promoter and a CDS.

Composite could then be used to link to a sub-diagram showing the two subcomponents.

4. Backwards Compatibility

The "User Defined" rectangle will be deprecated, then removed.

5. Discussion

References

Copyright

CC0
To the extent possible under law, SBOL developers has waived all copyright and related or neighboring rights to SEP V009. This work is published from: United States.

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cjmyers Oct 9, 2017

This looks good to me.

cjmyers commented Oct 9, 2017

This looks good to me.

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JS3xton Oct 13, 2017

Note: significant discussion on this topic has already occurred in SEP V006.


SBOL Visual Version: 1.1

I believe this should target SBOLv 2.0.

(Note: a discussion on the appropriate version was already started here)


The rectangle will also be eventually removed from Unspecified.

The Rectangle alternative will be deprecated and given RECOMMEND NOT status for Unspecified in SBOL Visual 1.1, then removed entirely in SBOL Visual 2.0.

The "User Defined" rectangle will be deprecated, then removed.

I will re-raise what I raised here and say:

  1. The Unspecified glyph is new (i.e. not currently present in the specification); I think we should simply introduce it with no specified alternatives (i.e. this SEP removes the rectangle glyph as a supported alternative for the Unspecified glyph and supersedes SEP V003, which declared the rectangle glyph as a valid alternative for the Unspecified glyph) rather than try to communicate that it has a deprecated alternative that will eventually be removed. I'm also not familiar with the "RECOMMEND NOT status"; isn't everything RECOMMENDED NOT that isn't RECOMMENDED or an accepted ALTERNATIVE?
  2. I don't understand precisely what "deprecation" means in the SBOL Visual context. How does that get realized?

JS3xton commented Oct 13, 2017

Note: significant discussion on this topic has already occurred in SEP V006.


SBOL Visual Version: 1.1

I believe this should target SBOLv 2.0.

(Note: a discussion on the appropriate version was already started here)


The rectangle will also be eventually removed from Unspecified.

The Rectangle alternative will be deprecated and given RECOMMEND NOT status for Unspecified in SBOL Visual 1.1, then removed entirely in SBOL Visual 2.0.

The "User Defined" rectangle will be deprecated, then removed.

I will re-raise what I raised here and say:

  1. The Unspecified glyph is new (i.e. not currently present in the specification); I think we should simply introduce it with no specified alternatives (i.e. this SEP removes the rectangle glyph as a supported alternative for the Unspecified glyph and supersedes SEP V003, which declared the rectangle glyph as a valid alternative for the Unspecified glyph) rather than try to communicate that it has a deprecated alternative that will eventually be removed. I'm also not familiar with the "RECOMMEND NOT status"; isn't everything RECOMMENDED NOT that isn't RECOMMENDED or an accepted ALTERNATIVE?
  2. I don't understand precisely what "deprecation" means in the SBOL Visual context. How does that get realized?
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cjmyers commented Oct 13, 2017

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I believe all of this is likely to be made moot by the likelihood of skipping SBOL 1.1 and going straight to SBOL 2.0, if we can get SEP V009 and SEP V010 passed.

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jakebeal commented Oct 13, 2017

I believe all of this is likely to be made moot by the likelihood of skipping SBOL 1.1 and going straight to SBOL 2.0, if we can get SEP V009 and SEP V010 passed.

@jakebeal jakebeal modified the milestones: SBOLv 2.0, SBOLv 1.1 Oct 28, 2017

@jakebeal jakebeal added Accepted and removed Draft labels Oct 31, 2017

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