datumObj ~
{
"subject" : SubjectObj,
"assay" : AssayObj,
"change" : ChangeString,
"treatement_type" : TreatmentTypeString, 
"treatment" : TreatmentObj,
"environment" : EnvironmentObj,
"times" : TimesObj,   // may be missing
"source" : SourceObj,
"extras" : Array[ExtraObj]
"meta": {
        "file": <source file name>,
        "line": Nat,
        "fulltext": <original datum text string>
    }
}

State datums have no treatement or treatment type entries

SubjectObj ~
{
  "entity" : ProteinString | GeneString,
  ("protein" : ProteinObj || "gene" : GeneString)
  "handle" : HandleString,
  "origin" : OriginString,  // default is "e"
  "ip" : IPString 
	}


GeneString -- declared in GENEOPS 
HandleString -- declared in HANDLEOPS
OriginString = {"null", "x", "e", "r", "p", "k"}
ProteinObj ~
{
 "protein" : ProteinString,
 "origin" : OriginString,
 "mutations" : array[mutationObj]         // may be missing if no mutations
 "modifications" : array[modificationObj] // ""
}

ProteinString -- declared in PROTEINOPS
ChangeString[irt,itpo,itao,by] = 
   {"increased", "decreased", "unchanged", "detectable-but unchanged"}
ChangeString[null] =  {"detectable","undetectable"}

mutationObj ~ 
{ 
  "mutation_type": MutationTypeString,  
  "text": MutationArgString,   
	"mutation_string" : String  //opetional
}

MutationTypeStrings and corresponding MutationArgStrings
"domain" ~ SeqInterval -- what is kept
"range" ~ XnnnY  -- point mutation string X,Y are aminoacid letters, nnn a seq pos
"del_domain" ~ SeqInterval -- what is deleted
"sym" ~ MutationConstant -- declared in ops/mutationops.maude

SeqInterval ~ (start-end)  start,end in Nat -- sequence positions

modificationObj ~
{
 "sym": ModificationSym  -- declared in ops/modificationops.maude
 "sites":  SequencePositionString
}


TreatmentTypeString = {"irt", "itpo", "itao", "by", ... }

TreatmentObj : 
  {
    "entities" : Array[EntityString],
    "treatements" : Array[TreatmentString | ProteinObj],
}
TreatmentString = ChemicalString | OProteinString | AntibodyString 
                  | PeptideString | StressString | SProteinString
EntityString = ChemicalString | ProteinString | AntibodyString 
                  | PeptideString | StressString 

allowed strings declared in ops files

TimesObj ~
 { "times" : Array[TLArrl], 
   "unit" : {"min","hr"}
 }

TLArr ~ [Nat,Nat] // [time,level]

SourceObj : {
 "pmid" : PMIDString,
 "figures" : FigureString,
}

EnvironmentObj : 
   {
    "cells" : CellString,  // declared in cellops
    "cell_mutations" : Array[CellMutationObj],
    "medium" : MediumString,
    "strings" : String
     }, 

CellMutationObj ~ NullMut | ProteinObj 

NullMut ~ (concat ProteinString "~null")


ExtraObj ~
 {
	"entities" : Array[EntityString], 
	"type" : ExtraTypeString,
  "adjective" : ExtraAdjectiveString,
  "mode" : ExtraModeString,
  "treatment" : TreatmentObj,
}

ExtraTypeString =
     {"unaffected by", "does not req", "enhanced by", "inhibited by", "reqs"},
ExtraModeString =
{"pretreatement", "preconditioning", "addition", "substitution" }


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
AssayObj =
   SimpleAssayObj | ModificationAssayObj |  BindingAssayObj | ActivationAssayObj 
 | LocationAssayObj| FractionAssayObj | ChipAssayObj| PhenotypeAssayObj

DetectionString --- declared in detectionops.maude 
    should have a file giving assay specific detection methods

SimpleAssayObj ~
 { "assay" :  SimpleAssayString, 
   "detect" : DetectionString }

SimpleAssayString =
   Gal4-reporter, mRNA, promo-reporter, internalization,
   nuc-export-reporter, nuc-import, nuc-export,
   surface-exp, prot-exp, prot-stability, secretion, reporter 
	 GXPAssayString, 	  REReporterAssayString, SimpleModAssayString
	 
GXPAssayString --  GTP-association,	GTP-hydrolysis, GDP-dissociation
REReporterAssayString ---   *-reporter
SimpleModAssayString ~ upshift, oligomerization, polymerization
--------------------------------

ModificationAssayObj
 { 
    "assay" : ModificationAssayString, 
    "detect" : DetectionString,
    "sites" : [SitesString] ,
    <sitetype> }

ModificationAssayString =
   { phos, acetyl, methyl, ubiq, sumo, nedd, cleavage }

SitesString -- / separated SiteString
SiteString -- declared in SITEOPS plus (AA num) constructions and "sitenr"
<sitetype> only relevant for phos ~ "phostype" : {"S", "T", "Y", "ST", "dual", "sitenr" }


--------------------------------
BindingAssayObj ~
 {
   "assay" : BindingAssayString,
   "detect" : DetectionString,
   "hooks" : Array[HookObj],
  }

BindingAssayString = {"boundby", "colocwith", "copptby", "snaggedby"}
HookObj ~
  {"entity" : HookEntityString, 
   "handle" : HandleString, 
    "origin" : OriginString 
		"protein" : ProteinObj
	}

HookEntityString =  ProteinString | PeptideString | ChemicalString 
                  | CompositeString | OligoString .


--------------------------------
ActivationAssayObj ~
 { 
   "assay" : ActivationAssayString,
   "detect" : DetectionString,
   "substrates" : Array[SubstrateString],
  }
|
 { 
   "assay" : "oligo-binding",
   "detect" : DetectionString,
   "oligo" : OligoString,
  }
 
OligoString -- declared in ASSAYOPS
ActivationAssayString = 
   {"IVKA", "IVLKA", "IVGefA", "IVPPaseAct", "IVHatAct", "IVProteaseAct"}

SubstrateString ~ ProteinString | PeptideString | ChemicalString 
                  | CompositeString | MiscSubstrateString
MiscSubstrateString ~ declared in ASSAYOPS


--------------------------------
LocationAssayObj
 {
   "assay" : "locatedin",
   "detect" : DetectionString,
   "position" : LocationString
}

--------------------------------
FractionAssayObj
 {
   "assay" : "infraction",
   "detect" : DetectionString,
   "fraction" : FractionString,
}

--------------------------------
ChipAssayObj
 {
   "assay" : "boundto",
   "detect" : "ChIP",
   "gene" : GeneString
}

PhenotypeAssayObj
 {
   "assay" : PhenotypeString,
   "detect" : DetectionString,
}

PhenotypeString ~ Apoptosis Proliferation G1Arrest receptor-binding