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incorporate Neil's comments

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jakebeal
jakebeal committed Nov 29, 2017
1 parent 2b36f6e commit 6fb5baf7c1ddebacd93d3f8429ad950b66c4cd60
Showing with 5 additions and 2 deletions.
  1. +5 −2 specification/language.tex
@@ -5,6 +5,9 @@ \section{SBOL Visual Diagram Language}
An SBOL Visual diagram represents information about the structure of a nucleic acid design and its associated molecular species and interactions.
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If desired, an SBOL Visual diagram may also be associated with a machine-interpretable model, such as SBOL, GenBank, or SBML.

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@jamesscottbrown

jamesscottbrown Nov 29, 2017

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I would suggest editing this slightly, as these are examples of model formats rather than models:

If desired, an SBOL Visual diagram may also be associated with a machine-interpretable model (e.g. in SBOL, GenBank, or SBML format).

@jamesscottbrown

jamesscottbrown Nov 29, 2017

Contributor

I would suggest editing this slightly, as these are examples of model formats rather than models:

If desired, an SBOL Visual diagram may also be associated with a machine-interpretable model (e.g. in SBOL, GenBank, or SBML format).

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@jakebeal

jakebeal Nov 30, 2017

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Thank you; fixed in c196935

@jakebeal

jakebeal Nov 30, 2017

Contributor

Thank you; fixed in c196935

In this document we describe the association for SBOL 2 data models, which provides a formal semantic grounding for all elements of an SBOL Visual diagram, but equivalent associations may be made between diagram elements and other models.
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In terms of SBOL 2 data models, the description of a nucleic acid design is formally defined as representation of a \sbol{ComponentDefinition} with a nucleic acid \sbol{type}, the \sbol{Component} and \sbol{SequenceAnnotation} objects describing the features and sub-structure of the design, and \sbol{SequenceConstraint} information on the relative positions of such elements.
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The description of interactions between some number of nucleic acid designs and other molecular species is formally defined as a representation of a \sbol{ModuleDefinition}, the \sbol{FunctionalComponent} objects describing the nucleic acid designs and other molecular species, and the \sbol{Interaction} and \sbol{Participation} objects describing their functional relationships.
@@ -150,15 +153,15 @@ \subsection{Nucleic Acid Sequence Features}
\subfigure[MAY]{\includegraphics[scale=0.5]{figures/examples/2f-custom.pdf}}
\subfigure[SHOULD NOT]{\includegraphics[scale=0.5]{figures/examples/2f-generic.pdf}}
\subfigure[MUST NOT]{\includegraphics[scale=0.5]{figures/examples/2f-conflict.pdf}}
\caption{Examples of recommended, allowed, and forbidden representation of a \sbol{ComponentDefinition} comprising a sequence of promoter, ribosome entry site, CDS, and terminator: (a) is RECOMMENDED because it uses the preferred variant of the most specific defined glyphs, (b) is allowed because it uses a custom non-conflicting symbol to encode more specific information about the particular CDS, (c) is recommended against because it uses less specific glyphs, and (d) is forbidden because it use a promoter symbol to represent the terminator.}
\caption{Examples of recommended, allowed, and forbidden representation of a \sbol{ComponentDefinition} comprising a sequence of promoter, ribosome entry site, CDS, and terminator: (a) is RECOMMENDED because it uses the preferred variant of the most specific defined glyphs, (b) is allowed because it uses some novel custom non-conflicting symbol, not matching any glyph defined in this document, to encode more specific information about the particular CDS, (c) is recommended against because it uses less specific glyphs, and (d) is forbidden because it use a promoter symbol to represent the terminator.}
\label{exa:2f}
\end{figure}
\end{enumerate}
\subsection{Molecular Species}
A glyph that is not in contact with any backbone represents any class of molecule whose detailed structure is not being shown using sequence feature glyphs.
In other words, either not a nucleic acid (e.g., proteins, small molecules) or else a nucleic acid whose structure is not being shown (e.g., an ``uninteresting'' mRNA coming from a CDS).
In other words, either not a nucleic acid (e.g., proteins, small molecules) or else an ``uninteresting'' nucleic acid (e.g., showing a transcribed mRNA, but not the features of its sequence).
In terms of SBOL 2 data models, this is a \sbol{FunctionalComponent} that is contained within a \sbol{ModuleDefinition} implicit in the diagram.
\begin{enumerate}

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