2. About the project
2
The Objectives of the project is to :
• Develop a Stoichiometry Plugin for Pathvisio.
• Improving validation through the PathVisio-
Validator plug-in.
• To Provide SBGN validation in the Validator -Plugin
and to update SBGN Plugin – to deal with ‘Auxiliary
Units’ issues.
3. Stoichiometry Plugin
3
The Plugin is aimed at producing a
Stoichiometry Matrix for a standard biological
Process Diagram(i.e the causal sequences of
molecular processes and their results).
4. Features:
4
• Generate a Stoichiometric Matrix for Process
Diagram .
• Can generate an “.txt” file containing Stoichiometry
Matrix .
11. Improving validation through the PathVisio-
Validator Plug-in
11
Created some new validation rules in
schematron to check valdations like:
• a logic arc should always connect to a logic gate, such as "OR" or
"AND“
• process nodes should have at least one input and at least one
ouput pointing to the arcs
• Whether a certain Glyph is allowed in PD,ER,AF languages
12. 12
Created some of the pass/fail test-cases
for Process Diagram, Activity Flow, Entity Relation
Languages.
Refer:
https://libsbgn.svn.sourceforge.net/svnroot/libsbgn/tru
13. To Provide SBGN validation in the Validator Plugin.
13
Earlier the Validator plugin was able to validate on
MIMML and GPML format, Hence I have enhanced the
functionality and provided the validation for SBGN format
too.
• Now theValidator Plugin automatically selects the ruleset
based on the format. Possible formats: GPML, MIMML,
SBGN-PD,ER,AF
14. Feature:
14
• we can simply choose to validate it, the plugin can
understand which format it is and validates
accordingly based on the format.
(or)
• We can explicitly validate the pathway against any of
the Ruleset (choosing Ruleset manually).