QUICK GUIDE TO BIOTAPESTRY CSV INPUT FORMAT
May 18, 2007 (Rev C)

*** Lines that begin with "#" are treated as comments.

Model instruction:

"model",modelName,parentModelName

Model hierarchy must form a tree; one and only one model has no parent
Model names must be unique


Region instruction:
            
"region",modelName,regionName,regionAbbreviation

Region name and abbreviation must be unique for a given model
Top level model cannot have regions
Abbreviation must be no longer than 3 characters


Interactions:

There are currently three types: general, signal, and nodeOnly.

NOTE: Though the following comma separated lists are
broken into several lines for clarity, they must occupy
only a single line in the CSV file.

General instructions:

nodeType = ["gene" | "bare" | "box" | "bubble" |
            "intercel" | "slash" | "diamond"]

interactionSign = ["positive" | "negative" | "neutral"]

"general",modelName,sourceNodeType,sourceNodeName,
          targetNodeType,targetNodeName,interactionSign,
          sourceRegionAbbrev,targetRegionAbbrev


Signal instructions:

signalType = ["promoteSig" | "repressSig" | "switchSig"]

    
"signal",modelName,"gene",signalSourceGeneName,"gene",targetGeneName,
         "gene",mediatedTranscriptionFactorName,signalType,
         sourceRegionAbbrev,targetRegionAbbrev

Node Only instructions:

nodeType = ["gene" | "bare" | "box" | "bubble" |
            "intercel" | "slash" | "diamond"]

"nodeOnly",modelName,nodeType,nodeName,regionAbbrev


A small example of an acceptable CSV file:

# models
"model","root"
"model","Endomesoderm Model","root"
"model","PMC Model","Endomesoderm Model"
"model","Endo Model","Endomesoderm Model"
# regions
"region","PMC Model","PMC","p"
"region","Endo Model","Endomesoderm","e"
# interactions
"general","Endo Model","gene","Krox","gene","Otx","positive","e","e"
"general","Endo Model","gene","Otx","gene","Bra","positive","e","e"
"general","Endo Model","gene","Otx","gene","FoxA","positive","e","e"
"general","Endo Model","gene","Otx","gene","GataE","positive","e","e"
"general","Endo Model","gene","GataE","gene","Otx","positive","e","e"
"general","Endo Model","gene","Otx","gene","Otx","positive","e","e"
"general","PMC Model","gene","Pmar","gene","Rmic","negative","p","p"
"general","PMC Model","gene","Rmic","gene","Delta","negative","p","p"
"general","PMC Model","gene","Rmic","gene","Tbr","negative","p","p"
"general","PMC Model","gene","Rmic","gene","Ets1","negative","p","p"
"general","PMC Model","gene","Rmic","gene","Alx1","negative","p","p"