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Commit bb0ad5c4 authored by Aishwarya Alex's avatar Aishwarya Alex
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Update README.md

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Convertor from xBEL to CellDesigner.
Input : .XBEL file (to be provided)
several mapping files already provided, can be updated to include any user defined entity mapping
Output : nodes.txt (nodes with anotation and location information)
reactions.txt (reactions, with nodes referring to nodes.txt and annotation)
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# Convertor from xBEL to CellDesigner.
## Input:
1. .XBEL file *(to be provided)*
Several mapping files already provided, can be updated to include any user defined entity mapping
2. abundanceMapping.txt : Mapping for abundance entities with namespaces
3. belSpeciesNestedAnnotationsMapping.txt : Mapping for nested elements, added as additional GO:annotation for elements eg: peptidaseActivity
4. desc2012.xml : MeSH xml file to create db, will be downloaded if doesn't exist
5. mesh_desc2012.txt : Will be created if doesn't exist, file to create sqlitedb
5. entityMapping.txt : Mapping for entity names from BEL to SBML
6. locationMapping.txt : Map for merging and mapping to location type: CELL, TISSUE or COMPARTMENT
7. namespaceMapping.txt : BEL namespaces to miriam urn mapping
8. reactionMapping.txt : BEL predicates to SBML reaction types
## Output:
nodes.txt (nodes with anotation and location information)
reactions.txt (reactions, with nodes referring to nodes.txt and annotation)
Usage:
xBCD=xBEL2CellD()
xBCD.convertXBEL('/home/alex/PhD/APP/Aetionomy_AD.xbel')
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