Skip to content
GitLab
Menu
Projects
Groups
Snippets
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Sign in
Toggle navigation
Menu
Open sidebar
Aishwarya Alex
xBELtoCellD
Commits
bb0ad5c4
Commit
bb0ad5c4
authored
Mar 07, 2018
by
Aishwarya Alex
Browse files
Update README.md
parent
d5e68217
Changes
1
Hide whitespace changes
Inline
Side-by-side
README.md
View file @
bb0ad5c4
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)
\ No newline at end of file
# 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')
\ No newline at end of file
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment