Update README.md

README.md

-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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