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Merge pull request #66 from SynBioDex/SEP-V015

Changes for SEP V015
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jakebeal committed May 10, 2019
2 parents bcb2042 + 57e7cfc commit 81acdd009e8ad035e7bd7fa59605d02898543473
@@ -1,7 +1,7 @@
# Complex

## Associated BioPAX term(s)
Complex: http://www.biopax.org/release/biopax-level3.owl#Complex
## Associated SBO term(s)
SBO:0000253 Non-covalent complex

## Recommended Glyph and Alternates
The RECOMMENDED glyph for a complex is a composite of the glyphs for the molecules of comprising the complex. For example, a protein bound to a small molecule, a guide RNA, or another protein:
@@ -19,4 +19,4 @@ An alternative is the SBGN "cornered rectangle" glyph for a complex:
Arabinose bound to AraC

## Notes
*This section left intentionally blank*
Alternate BioPAX definition: Complex: http://www.biopax.org/release/biopax-level3.owl#Complex
@@ -1,7 +1,7 @@
# Double-Stranded Nucleic Acid

## Associated BioPAX term(s)
Dna: http://www.biopax.org/release/biopax-level3.owl#Dna
## Associated SBO term(s)
SBO:0000251 Deoxyribonucleic acid

## Recommended Glyph and Alternates
The RECOMMENDED glyph for dsNA is a double-helix:
@@ -17,4 +17,4 @@ An alternative is the SBGN "nucleic acid" half-round rectangle:
DNA fragment during assembly

## Notes
*This section left intentionally blank*
Alternate BioPAX definition: Dna: http://www.biopax.org/release/biopax-level3.owl#Dna
@@ -1,7 +1,7 @@
# Macromolecule

## Associated BioPAX term(s)
Protein: http://www.biopax.org/release/biopax-level3.owl#Protein
## Associated SBO term(s)
SBO:0000245 Macromolecule

## Recommended Glyph and Alternates
The macromolecule glyph is a diagonally offset union of a large and small circle, intended to invoke the complex shapes of proteins:
@@ -17,4 +17,4 @@ An alternative is the SBGN macromolecule glyph, a rounded rectangle:
AraC

## Notes
It is unclear whether this should be just "Protein" or whether we also want it to be able to repesent multi-component elements like a protein composed of multiple sub-units or a complex polymer.
Note that this also covers BioPAX term Protein: http://www.biopax.org/release/biopax-level3.owl#Protein
@@ -1,7 +1,7 @@
# No Glyph Assigned

## Associated BioPAX term(s)
Any BioPAX type that is not covered by any glyph besides the root
## Associated SBO term(s)
Any SBO type that is not covered by any glyph besides the root

## Recommended Glyph and Alternates
When a species has no assigned glyph it is RECOMMENDED that a user provide their own glyph. The user is also encouraged to submit the new glyph for possible adoption into the SBOLv standard.
@@ -1,7 +1,7 @@
# Small Molecule
# Simple Chemical

## Associated BioPAX term(s)
Small Molecule: http://www.biopax.org/release/biopax-level3.owl#SmallMolecule
## Associated SBO term(s)
SBO:0000247 Simple chemical

## Recommended Glyph and Alternates
The small molecule glyph is a circle that stretches sideways into a "stadium" to accomodate longer names:
@@ -13,4 +13,4 @@ The small molecule glyph is a circle that stretches sideways into a "stadium" to
Arabinose

## Notes
*This section left intentionally blank*
Alternate BioPAX definition: Small Molecule: http://www.biopax.org/release/biopax-level3.owl#SmallMolecule
@@ -1,7 +1,7 @@
# Single-Stranded Nucleic Acid

## Associated BioPAX term(s)
Rna: http://www.biopax.org/release/biopax-level3.owl#Rna
## Associated SBO term(s)
SBO:0000250 Ribonucleic acid

## Recommended Glyph and Alternates
The RECOMMENDED glyph for ssNA is a wiggly line:
@@ -17,4 +17,4 @@ An alternative is the SBGN "nucleic acid" half-round rectangle:
mRNA, gRNA, siRNA

## Notes
*This section left intentionally blank*
Alternate BioPAX definition: Rna: http://www.biopax.org/release/biopax-level3.owl#Rna
@@ -1,7 +1,7 @@
# Unspecified

## Associated BioPAX term(s)
PhysicalEntity: http://www.biopax.org/release/biopax-level3.owl#PhysicalEntity
## Associated SBO term(s)
SBO:0000285 Material entity of unspecified nature

## Recommended Glyph and Alternates
Unspecified is RECOMMENDED to be represented by the unicode "replacement character" glyph, indicating a missing or invalid symbol:
@@ -19,3 +19,4 @@ An anonymous chemical species that is missing any information about its nature o
## Notes
The Unspecified glyph is intended for showing where a chemical species' type is missing (or, equivalently, given only the uninformative root role). It should never appear with well-curated designs or diagrams.

Alternate BioPAX definition: PhysicalEntity: http://www.biopax.org/release/biopax-level3.owl#PhysicalEntity
@@ -13,7 +13,7 @@ \section{SBOL Glyphs}\label{sec:glyphs}
\item {\bf Sequence Feature Glyphs} describe features of nucleic acid sequences. They are associated with Sequence Ontology terms.
For the SBOL 2 data model, this is formally defined as any \sbol{Component} with a compatible term within its associated \sbol{roles},
i.e., one that is equal to or a child of at least one term associated with the glyph.
\item {\bf Molecular Species Glyphs} represent any class of molecule whose detailed structure is not being shown using sequence feature glyphs. They are associated with BioPAX terms. For the SBOL 2 data model, this is formally defined as any \sbol{FunctionalComponent} with a compatible term within its associated \sbol{types},
\item {\bf Molecular Species Glyphs} represent any class of molecule whose detailed structure is not being shown using sequence feature glyphs. They are associated with \twotwozero{Systems Biology Ontology} terms. For the SBOL 2 data model, this is formally defined as any \sbol{FunctionalComponent} with a compatible term within its associated \sbol{types},
i.e., one that is equal to or a child of at least one term associated with the glyph.
\item {\bf Interaction Glyphs} are ``arrows'' indicating functional relationships between sequence features and/or molecular species. They are associated with Systems Biology Ontology terms.
For the SBOL 2 data model, this is formally defined as any \sbol{Interaction} with a compatible term within its \sbol{types},
@@ -46,7 +46,7 @@ \subsection{Requirements for Glyphs}
be constructed:
\begin{enumerate}
\item A glyph SHOULD have its meaning defined by associating the glyph with at least one ontology definition.
Definitions are RECOMMENDED to be from the Sequence Ontology for nucleic acid components, from BioPAX for other components, and from the Systems Biology Ontology for interactions.
Definitions are RECOMMENDED to be from the Sequence Ontology for sequence feature glyphs, from the \twotwozero{Systems Biology Ontology for molecular species glyphs}, and from the Systems Biology Ontology for interaction glyphs.
If no applicable terms are available in the preferred ontology, proposal of a new glyph SHOULD be accompanied by a request to the ontology maintainers to add a term for the undefined entity.
\item A glyph SHOULD be relatively easy to sketch by hand (e.g., no high-complexity images or precise angles required).
\item A glyph specification MUST indicate which portions of the glyph are the ``interior'' for purposes of color fill.
@@ -13,7 +13,7 @@
\usepackage[final]{pdfpages}

% putting versions on changebars
\newcommand{\version}[1]{\marginpar{\hspace*{34pt}\raisebox{-3.0ex}{\color{red}\small #1}}}
\newcommand{\version}[2]{\marginpar{\hspace*{34pt}\raisebox{-3.0ex}{\color{#1}\small #2}}}

%% ============================================================================
%% Description: Documentation for sbmlpkgspec.cls
@@ -119,7 +119,7 @@
\cbcolor{red}
\cbstart%
{\color{red}%
\version{2.1.0}%
\version{red}{2.1.0}%
#1
}
\cbend
@@ -138,8 +138,8 @@
\newcommand{\twotwozero}[1]{%
\cbcolor{magenta}
\cbstart%
{\color{red}%
\version{2.2.0}%
{\color{magenta}%
\version{magenta}{2.2.0}%
#1
}
\cbend

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