Re: [SynBioDex/SBOL-visual] Need a new symbol for "other" SO terms (#14)

[Chris Myers]

Ok, below is a concrete example of the problem we face in designer.  In the first screenshot, the User-defined symbol is used for hierarchy to indicate an “Engineered Region” that has multiple functions (i.e., an RBS and CDS). 

In the second screenshot, we see a file converted from GenBank.  Here the user-defined shows up because there are several features in the GenBank file that do not map to glyphs in SBOL Visual.

To me, these are fundamentally different from both a visualization perspective and UI perspective.  In one case, the visualization is telling you there is more details that are hidden while in the other it is telling you that there are parts that you don’t know how to render in a specific way.  These are simply different messages and using one image to convey both messages is confusing.  

On Aug 2, 2016, at 1:56 PM, bbartley <notifi...@github.com> wrote:

Another approach for indicating hierarchical composition that I have contemplated is using some kind of an accent mark (eg, a caret) over or under a glyph to suggest the component contains substructure.  This translates equally well for user-defined or explicit components (eg, promoter).  It is simple to draw by hand and would make sense in a UI.  Also it would lend a "linguistic" flavor to SBOLv.

From: Jacob Beal <notifi...@github.com>
To: SynBioDex/SBOL-visual <SBOL-...@noreply.github.com>
Cc: bbartley <bart...@yahoo.com>; Comment <com...@noreply.github.com>
Sent: Tuesday, August 2, 2016 12:45 PM
Subject: Re: [SynBioDex/SBOL-visual] Need a new symbol for "other" SO terms (#14)

I would represent this case with a label on the user-defined that says: "payload"—
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[Jacob Beal]

For my own perspective, I view *anything* above the level of sequence as having hidden details, and thus still find there to be no significant distinction between the two cases.  

Let me try to articulate my objection a bit further, as well, since I'm realizing that this feels to me like an issue of breaking abstraction.  If we add a symbol for "Has hierarchical substructure," it will be the *only* symbol in SBOL visual that is not communicating about biology.  Every other symbol that we have is independent of representational choice, but describes some physical property of the system that we are describing.  This symbol, on the other hand, is a meta-symbol that describes only how we are describing biology, and then only if we don't have a more succinct way of describing the sequence. Thus, if we add this symbol, then it means that you can't tell if you've diagrammed something correctly unless you have access to a full SBOL data representation of the object, which we don't have in many cases (e.g., whiteboard sketch; partial object retrieval).  It also means that the symbol may be correct but then become incorrect if we add more information, which also feels problematic to me.

Now, I see no problem with specific tooling adding visual annotations (like Bryan's suggestion of some sort of carat symbol) to communicate to a user when substructure information is available about a diagram element --- any diagram element, not just "user defined."  I am extremely dubious, however, about adding this special-case glyph, since I see it having vast and potentially problematic implications.

Thanks,

-Jake

[Chris J. Myers]

But actually what I'm asking for is a glyph for a specific so term and branch: engineered region.

You are correct that this and any glyph may or may not have substructure which is fine. This one usually will.

So I see this request as completely consistent with other requests for glyphs for specific so terms.

Chris

Sent from my iPhone

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[Jacob Beal]

Well, please feel free to make a specific proposal, and we'll see if it can draw support.

Thanks,

-Jake

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[Bryan Bartley]

Hi Jake,

As you requested, here are two examples of how I might use an accent mark to indicate hierarchy, both hand drawn and machine drawn.

Best

Bryan

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