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AF_phenotype.xml
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<mediawiki xmlns="http://www.mediawiki.org/xml/export-0.3/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.mediawiki.org/xml/export-0.3/ http://www.mediawiki.org/xml/export-0.3.xsd" version="0.3" xml:lang="en">
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<sitename>sbgn.org</sitename>
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<page>
<title>AF phenotype</title>
<id>683</id>
<revision>
<id>2801</id>
<timestamp>2012-05-25T07:53:13Z</timestamp>
<contributor>
<username>Huaiyumi</username>
<id>18</id>
</contributor>
<comment>/* AF phenotype glyph survey */</comment>
<text xml:space="preserve">== AF phenotype glyph survey ==
In SBGN Activity Flow, ''phenotype'' and ''perturbation'' are both activity nodes, and are represented by glyphs identical to those of ''perturbing agent'' and ''phenotype'' in PD, respectively. The syntax of both glyphs is identical to that in PD also, i.e., ''perturbation'' can only be the source of an influence arc, and ''phenotype'' can only be the target.
There are two issues related to this.
1. In PD, ''perturbing agent'' is an EPN, while ''phenotype'' is a process node, while in AF, both ''perturbation'' and ''phenotype'' are activity nodes (processes). Using the same glyph for two semantically different concept is confusing.
2. In AF, sometime a ''phenotype'' can be a source of the different arc, for example, Na channel activity -> membrane depolarization -> K channel activity -> membrane repolarization. The current AF syntax makes it difficult to represent such pathways.
The topic was discussed at the HARMONY in April, and a few solutions have been suggested, which are summarized below.
'''A. Solution for the glyph of ''perturbation'''''
Remove ''perturbation'' as an activity node. Instead, use it as a decoration of an activity node like ''macromolecule'' or ''nucleic acid feature''.
Examples: the [[Media: Perturbation.png|glyph]], [[Media: PPAR-perturbation.png|PPAR pathway]].
'''B. Solutions of ''phenotype'''''
Below is a summary of the suggestions gathered at the HARMONY
1. Remove ''phenotype'' glyph, and use ''activity node'' to represent it.
*[[Media: Phenotype_proposal1.png|Example]]
*Problem: It loses the specificity to represent something that is observed.
2. Remove ''phenotype'' glyph, use ''activity node'' with a specific decoration that reflects the fact that it can be observed.
*[[Media: Phenotype_proposal2.png|Example]]
*Problem: a new glyph has to be designed, and its meaning is similar to that of ''phenotype''.
3. Remove ''phenotype'' glyph, use ''activity node'' with a ''phenotype'' glyph as a decoration.
*[[Media: Phenotype_proposal3.png|Example]]
*Problem: ''phenotype'' glyph is a process node in PD, and semantically it should not be used as a decoration.
4. Keep ''phenotype'' glyph, and it can only be the output of an influence arc, but design a new influence arc such as “causation”.
*[[Media: Phenotype_proposal4.png|Example]]
*Problem: need to create a new arc glyph and its meaning could potentially be the same as existing ones.
5. Allow ''phenotype'' glyph to be both input and output of influence arcs.
*[[Media: Penotype_proposal5.png|Example]]
*Problem: It is not consistent with that of PD. In PD, a ''phenotype'' can only be the boundary of the pathway, i.e., the target of an arc.
6. Keep the current spec, i.e., ''phenotype'' glyph can only be the output of an arc.
Results of the voting.
1 vote - proposal 1
1 vote - proposal 2
0 vote - proposal 3
0 vote - proposal 4
3 votes - proposal 5
2 votes - proposal 6
No decision was made. Need further discussion.</text>
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