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ucfToSBOL.js
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ucfToSBOL.js
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//Dependencies
var fs = require('fs');
var SBOLDocument = require('sboljs');
//IO Locations
var ucfFilepath = 'ucf/Eco1C1G1T0.UCF.json';
var resultFolder = 'result/';
var cytometryFolder = resultFolder + 'cytometry/';
var toxicityFolder = resultFolder + 'toxicity/';
var resultSBOL = resultFolder + 'cello.xml';
//Constant Terms
const version = '1-Eco1C1G1T0';
const urlprefix = 'http://cellocad.org/';
const derivedFrom = 'https://github.com/CIDARLAB/cello/blob/master/resources/UCF/Eco1C1G1T0.UCF.json';
const datecreated = new Date("April 1, 2016 00:00:00");
const today = new Date();
var terms = SBOLDocument.terms;
var so = 'http://identifiers.org/so/'
var sbo = 'http://identifiers.org/biomodels.sbo/';
const provNS = 'http://www.w3.org/ns/prov#';
const dcNS = 'http://purl.org/dc/elements/1.1/';
const ownedBy = 'http://wiki.synbiohub.org/wiki/Terms/synbiohub#/ownedBy';
const productionSO = sbo + 'SBO:0000589';
const inhibitionSO = sbo + 'SBO:0000169';
const inhibitorSO = sbo + 'SBO:0000020';
const inhibitedSO = sbo + 'SBO:0000642';
const templateSO = sbo + 'SBO:0000645';
const productSO = sbo + 'SBO:0000011';
const regulatorSO = sbo + 'SBO:0000369';
//const tetrFamilySO = so + 'SO:0000187'; //SO for repeat sequences.
var celloSO = 'http://wiki.synbiohub.org/wiki/Terms/cello#';
const ymax = celloSO + 'ymax';
const ymin = celloSO + 'ymin';
const n = celloSO + 'n';
const kd = celloSO + 'K';
const eqn = celloSO + 'response-function';
const gate_type = celloSO + 'gate_type';
const color_hexcode = celloSO + 'gate-color-hexcode';
const group_name = celloSO + 'group-name';
const tetR_family = celloSO + 'family'
const gate_parts_so = 'http://identifiers.org/so/SO:0000804';
//var activityURI = 'https://synbiohub.programmingbiology.org/public/Cello_Parts/cello2sbol/1';
//Create a new SBOL Document
var sbol = new SBOLDocument();
//Only Required while creating this the first time.
//Create an Activity - A conversion script
var actVersion = 1;
var actDisplayId = 'cello2sbol';
var actPersistantIdentity = urlprefix + actDisplayId;
var activityURI = actPersistantIdentity + '/' + actVersion;
const activity = sbol.genericTopLevel(activityURI, provNS + 'Activity');
activity.version = actVersion;
activity.displayId = actDisplayId;
activity.name = 'Cello UCF to SBOL conversion';
activity.description = 'Conversion of the Cello UCF parts and metadata to SBOL2.1';
activity.addStringAnnotation(dcNS + 'creator', 'Prashant Vaidyanathan');
activity.addStringAnnotation(dcNS + 'creator', 'Chris J. Myers');
activity.addStringAnnotation('http://purl.org/dc/terms/created', today.toISOString() + '');
activity.persistentIdentity = actPersistantIdentity;
activity.uri = activityURI;
//Load the Cello UCF File
var ucf = JSON.parse(fs.readFileSync(ucfFilepath) + '');
//Arrays and Maps to store each JSON collection object in the UCF
var gate_partsArr = [];
var response_funcMap = {};
var partsMap = {};
var partsSBOL = {}
var moduleDefnMap = {}
var cytometryMap = {};
var toxicityMap = {};
var gatesMap = {};
var motif_library = [];
var logicConstraints;
var eugeneRules;
var geneticLocations;
var measurementstd;
var header;
//Go through the UCF file to store collections in local data structures (arrays and maps)
ucf.forEach(function (collection) {
switch (collection.collection) {
case 'parts':
//partsArr.push(collection);
partsMap[collection.name] = collection;
break;
case 'gate_parts':
gate_partsArr.push(collection);
break;
case 'response_functions':
response_funcMap[collection.gate_name] = collection;
break;
case 'gates':
gatesMap[collection.gate_name] = collection;
break;
case 'gate_cytometry':
cytometryMap[collection.gate_name] = collection.cytometry_data;
break;
case 'gate_toxicity':
toxicityMap[collection.gate_name] = collection;
break;
case 'motif_library':
motif_library.push(collection);
break;
case 'logic_constraints':
logicConstraints = collection;
break;
case 'eugene_rules':
eugeneRules = collection;
break;
case 'genetic_locations':
geneticLocations = collection;
break;
case 'measurement_std':
measurementstd = collection;
break;
case 'header':
header = collection;
break;
}
}, this);
//Function calls to create the SBOL Document
convertPartsToSBOL();
convertGatePartsToSBOL();
//Function calls to create attachments
convertCytometryToAttachments();
covertToxicityToAttachments();
createCircuitConstraintsFile();
//Write the SBOL document to an XML file.
fs.writeFile(resultSBOL, sbol.serializeXML(), function (err) {
if (err) {
return console.log(err);
}
console.log("Cello SBOL file created!");
});
//Function to convert Cello Parts to SBOL
function convertPartsToSBOL() {
Object.keys(partsMap).forEach(function (partkey) {
var part = partsMap[partkey];
var partName = part.name;
if (!(partName in partsSBOL)) {
const componentDefinition = sbol.componentDefinition()
componentDefinition.version = version;
componentDefinition.displayId = part.name;
componentDefinition.name = part.name;
componentDefinition.persistentIdentity = urlprefix + componentDefinition.displayId;
componentDefinition.uri = componentDefinition.persistentIdentity + '/' + componentDefinition.version;
componentDefinition.wasDerivedFrom = derivedFrom;
componentDefinition.addUriAnnotation(provNS + 'wasGeneratedBy', activityURI);
const sequence = sbol.sequence()
sequence.displayId = part.name + '_sequence';
sequence.name = part.name + '_sequence';
sequence.version = version;
sequence.elements = part.dnasequence;
sequence.persistentIdentity = urlprefix + sequence.displayId;
sequence.uri = sequence.persistentIdentity + '/' + sequence.version;
sequence.wasDerivedFrom = derivedFrom;
sequence.encoding = SBOLDocument.terms.dnaSequence;
sequence.addUriAnnotation(provNS + 'wasGeneratedBy', activityURI);
componentDefinition.addSequence(sequence)
componentDefinition.addRole(getPartType(part.type));
componentDefinition.addType(SBOLDocument.terms.dnaRegion);
// Create a Protein
if (part.type === 'cds') {
const proteinComponentDefinition = sbol.componentDefinition();
proteinComponentDefinition.version = version;
proteinComponentDefinition.displayId = componentDefinition.displayId + '_protein';
proteinComponentDefinition.name = componentDefinition.displayId + '_protein';
proteinComponentDefinition.persistentIdentity = urlprefix + proteinComponentDefinition.displayId;
proteinComponentDefinition.uri = proteinComponentDefinition.persistentIdentity + '/' + proteinComponentDefinition.version;
proteinComponentDefinition.addType(SBOLDocument.terms.protein);
proteinComponentDefinition.addUriAnnotation(provNS + 'wasGeneratedBy', activityURI);
partsSBOL[partName + '_protein'] = proteinComponentDefinition.uri;
const moduleDefinition = sbol.moduleDefinition();
moduleDefinition.name = proteinComponentDefinition.displayId + '_production';
moduleDefinition.version = version;
moduleDefinition.displayId = proteinComponentDefinition.displayId + '_production';
moduleDefinition.persistentIdentity = urlprefix + moduleDefinition.displayId;
moduleDefinition.uri = moduleDefinition.persistentIdentity + '/' + moduleDefinition.version;
moduleDefinition.addUriAnnotation(provNS + 'wasGeneratedBy', activityURI);
//Functional Component for Coding sequence
const functionalComponentCDS = sbol.functionalComponent();
functionalComponentCDS.version = version;
functionalComponentCDS.displayId = componentDefinition.displayId + '_functionalComponent';
functionalComponentCDS.name = componentDefinition.name + '_functionalComponent';
functionalComponentCDS.persistentIdentity = moduleDefinition.persistentIdentity + '/' + functionalComponentCDS.displayId;
functionalComponentCDS.uri = functionalComponentCDS.persistentIdentity + '/' + functionalComponentCDS.version;
functionalComponentCDS.definition = componentDefinition;
//Functional Component for Protein
const functionalComponentProt = sbol.functionalComponent();
functionalComponentProt.version = version;
functionalComponentProt.displayId = proteinComponentDefinition.displayId + '_functionalComponent';
functionalComponentProt.name = proteinComponentDefinition.name + '_functionalComponent';
functionalComponentProt.persistentIdentity = moduleDefinition.persistentIdentity + '/' + functionalComponentProt.displayId;
functionalComponentProt.uri = functionalComponentProt.persistentIdentity + '/' + functionalComponentProt.version;
functionalComponentProt.definition = proteinComponentDefinition;
//CDS to Protein interaction
const interaction = sbol.interaction();
interaction.displayId = proteinComponentDefinition.displayId + '_interaction';
interaction.name = interaction.displayId;
interaction.version = version;
interaction.persistentIdentity = moduleDefinition.persistentIdentity + '/' + interaction.displayId;
interaction.uri = interaction.persistentIdentity + '/' + interaction.version;
interaction.addType(productionSO);
//CDS Participation
const participationCDS = sbol.participation();
participationCDS.version = version;
participationCDS.name = componentDefinition.displayId + '_participation';
participationCDS.displayId = componentDefinition.displayId + '_participation';
participationCDS.persistentIdentity = interaction.persistentIdentity + '/' + participationCDS.displayId;
participationCDS.uri = participationCDS.persistentIdentity + '/' + participationCDS.version;
participationCDS.addRole(templateSO);
participationCDS.participant = functionalComponentCDS;
//Protein Participation
const participationProt = sbol.participation();
participationProt.version = version;
participationProt.name = proteinComponentDefinition.displayId + '_participation';
participationProt.displayId = proteinComponentDefinition.displayId + '_participation';
participationProt.persistentIdentity = interaction.persistentIdentity + '/' + participationProt.displayId;
participationProt.uri = participationProt.persistentIdentity + '/' + participationProt.version;
participationProt.addRole(productSO);
participationProt.participant = functionalComponentProt;
interaction.addParticipation(participationCDS);
interaction.addParticipation(participationProt);
moduleDefinition.addFunctionalComponent(functionalComponentCDS);
moduleDefinition.addFunctionalComponent(functionalComponentProt);
moduleDefinition.addInteraction(interaction);
}
componentDefinition.addStringAnnotation('http://purl.org/dc/terms/created', datecreated.toISOString() + '');
var uriVal = componentDefinition.uri;
partsSBOL[partName] = uriVal;
}
}, this);
};
//Function to convert Cello Gate Parts to SBOL
function convertGatePartsToSBOL() {
gate_partsArr.forEach(function (gpart) {
var gpartName = gpart.gate_name;
const componentDefinition = sbol.componentDefinition();
componentDefinition.version = version;
componentDefinition.displayId = gpartName;
componentDefinition.name = gpartName;
componentDefinition.persistentIdentity = urlprefix + componentDefinition.displayId;
componentDefinition.uri = componentDefinition.persistentIdentity + '/' + componentDefinition.version;
componentDefinition.wasDerivedFrom = derivedFrom;
componentDefinition.addUriAnnotation(provNS + 'wasGeneratedBy', activityURI);
//add information from Gates Collection
componentDefinition.addStringAnnotation(tetR_family, gatesMap[gpartName].system);
//componentDefinition.addUriAnnotation(regulatorSO, gatesMap[gpartName].regulator);
componentDefinition.addStringAnnotation(group_name, gatesMap[gpartName].group_name);
componentDefinition.addStringAnnotation(gate_type, gatesMap[gpartName].gate_type );
componentDefinition.addStringAnnotation(color_hexcode, gatesMap[gpartName].color_hexcode);
//Cassette parts in Gate
gpart.expression_cassettes.forEach(function (expression_cassettesArr) {
var seq = "";
var annotationCount = 0;
var start = 1;
expression_cassettesArr.cassette_parts.forEach(function (cassette) {
const component = sbol.component();
component.version = version;
component.displayId = cassette;
component.name = cassette;
component.persistentIdentity = componentDefinition.persistentIdentity + '/' + component.displayId;
component.uri = component.persistentIdentity + '/' + component.version;
component.definition = sbol.lookupURI(partsSBOL[cassette]);
componentDefinition.addComponent(component);
var cass_seq = partsMap[cassette].dnasequence;
seq += cass_seq;
const sa = sbol.sequenceAnnotation();
sa.displayId = 'annotation' + annotationCount;
annotationCount++;
sa.name = cassette;
sa.version = version;
sa.persistentIdentity = componentDefinition.persistentIdentity + '/' + sa.displayId;
sa.uri = sa.persistentIdentity + '/' + sa.version;
sa.component = component;
sa.description = partsMap[cassette].type;
const range = sbol.range();
range.displayId = 'range';
range.persistentIdentity = sa.persistentIdentity + '/' + range.displayId;
range.version = version;
range.uri = range.persistentIdentity + '/' + range.version;
range.start = start;
var end = start + cass_seq.length - 1;
range.end = end;
range.orientation = 'http://sbols.org/v2#inline';
sa.addLocation(range);
componentDefinition.addSequenceAnnotation(sa);
//Create Protein -> Promoter repression Module definition
if (partsMap[cassette].type === 'cds') {
if (!(cassette in moduleDefnMap)) {
const moduleDefinition = sbol.moduleDefinition();
moduleDefinition.version = version;
moduleDefinition.name = cassette + '_' + gpart.promoter + '_repression';
moduleDefinition.displayId = cassette + '_' + gpart.promoter + '_repression';
moduleDefinition.persistentIdentity = urlprefix + moduleDefinition.displayId;
moduleDefinition.uri = moduleDefinition.persistentIdentity + '/' + moduleDefinition.version;
moduleDefinition.addUriAnnotation(provNS + 'wasGeneratedBy', activityURI);
//Functional Component for Protein
const functionalComponentCDS = sbol.functionalComponent();
functionalComponentCDS.version = version;
functionalComponentCDS.name = cassette + '_protein_functionalComponent';
functionalComponentCDS.displayId = cassette + '_protein_functionalComponent';
functionalComponentCDS.persistentIdentity = moduleDefinition.persistentIdentity + '/' + functionalComponentCDS.displayId;
functionalComponentCDS.uri = functionalComponentCDS.persistentIdentity + '/' + functionalComponentCDS.version;
functionalComponentCDS.definition = sbol.lookupURI(partsSBOL[cassette + '_protein']);
//Functional Component for Promoter
const functionalComponentProm = sbol.functionalComponent();
functionalComponentProm.version = version;
functionalComponentProm.name = gpart.promoter + '_functionalComponent';
functionalComponentProm.displayId = gpart.promoter + '_functionalComponent';
functionalComponentProm.persistentIdentity = moduleDefinition.persistentIdentity + '/' + functionalComponentProm.displayId;
functionalComponentProm.uri = functionalComponentProm.persistentIdentity + '/' + functionalComponentProm.version;
functionalComponentProm.definition = sbol.lookupURI(partsSBOL[gpart.promoter]);
//Protein -> Promoter Interaction
const interaction = sbol.interaction();
interaction.version = version;
interaction.name = cassette + '_' + gpart.promoter + '_interaction';
interaction.displayId = cassette + '_' + gpart.promoter + '_interaction';
interaction.persistentIdentity = moduleDefinition.persistentIdentity + '/' + interaction.displayId;
interaction.uri = interaction.persistentIdentity + '/' + interaction.version;
interaction.addType(inhibitionSO);
//Protein participation
const participantProt = sbol.participation();
participantProt.version = version;
participantProt.name = cassette + '_protein_participation';
participantProt.displayId = cassette + '_protein_participation';
participantProt.persistentIdentity = interaction.persistentIdentity + '/' + participantProt.displayId;
participantProt.uri = participantProt.persistentIdentity + '/' + participantProt.version;
participantProt.addRole(inhibitorSO);
participantProt.participant = functionalComponentCDS;
//Promoter participation
const participantProm = sbol.participation();
participantProm.version = version;
participantProm.name = gpart.promoter + '_participation';
participantProm.displayId = gpart.promoter + '_participation';
participantProm.persistentIdentity = interaction.persistentIdentity + '/' + participantProm.displayId;
participantProm.uri = participantProm.persistentIdentity + '/' + participantProm.version;
participantProm.addRole(inhibitedSO);
participantProm.participant = functionalComponentProm;
interaction.addParticipation(participantProt);
interaction.addParticipation(participantProm);
moduleDefinition.addFunctionalComponent(functionalComponentCDS);
moduleDefinition.addFunctionalComponent(functionalComponentProm);
moduleDefinition.addInteraction(interaction);
moduleDefnMap[cassette] = gpart.promoter;
}
}
start += cass_seq.length;
});
const sequence = sbol.sequence()
sequence.displayId = gpartName + '_sequence';
sequence.name = gpartName + '_sequence';
sequence.version = version;
sequence.elements = seq;
sequence.persistentIdentity = urlprefix + sequence.displayId;
sequence.uri = sequence.persistentIdentity + '/' + sequence.version;
sequence.wasDerivedFrom = derivedFrom;
sequence.encoding = SBOLDocument.terms.dnaSequence;
sequence.addUriAnnotation(provNS + 'wasGeneratedBy', activityURI);
componentDefinition.addSequence(sequence);
}, this);
response_funcMap[gpartName].parameters.forEach(function (param) {
switch (param.name) {
case 'ymax':
componentDefinition.addStringAnnotation(ymax, param.value);
break;
case 'ymin':
componentDefinition.addStringAnnotation(ymin, param.value);
break;
case 'K':
componentDefinition.addStringAnnotation(kd, param.value);
break;
case 'n':
componentDefinition.addStringAnnotation(n, param.value);
break;
}
}, this);
componentDefinition.addStringAnnotation(eqn, response_funcMap[gpartName].equation);
componentDefinition.addType(SBOLDocument.terms.dnaRegion);
componentDefinition.addRole(gate_parts_so);
componentDefinition.addStringAnnotation('http://purl.org/dc/terms/created', datecreated.toISOString() + '');
}, this);
};
function convertCytometryToAttachments() {
Object.keys(cytometryMap).forEach(function (cytometry) {
var cytometry_filepath = cytometryFolder + cytometry + '_cytometry.json';
fs.writeFile(cytometry_filepath, JSON.stringify(cytometryMap[cytometry], null, 2), function (err) {
if (err) {
return console.log(err);
}
console.log("Cytometry file for " + cytometry + " created!");
});
}, this);
}
function covertToxicityToAttachments() {
Object.keys(toxicityMap).forEach(function (toxicity) {
var toxicity_filepath = toxicityFolder + toxicity + '_toxicity.json';
var toxMap = {};
toxMap['input'] = toxicityMap[toxicity].input;
toxMap['growth'] = toxicityMap[toxicity].growth;
fs.writeFile(toxicity_filepath, JSON.stringify(toxMap, null, 2), function (err) {
if (err) {
return console.log(err);
}
console.log("Toxicity file for " + toxicity + " created!");
});
}, this);
}
function createCircuitConstraintsFile() {
var constraints = {};
constraints['logic_constraints'] = logicConstraints;
constraints['motif_library'] = motif_library;
constraints['eugene_rules'] = eugeneRules;
constraints['genetic_locations'] = geneticLocations;
constraints['measurement_std'] = measurementstd;
constraints['header'] = header;
var circuitConstraintsFilepath = resultFolder + 'circuitConstraints.json'
fs.writeFile(circuitConstraintsFilepath, JSON.stringify(constraints, null, 2), function (err) {
if (err) {
return console.log(err);
}
console.log("Circuit constraints file created!");
});
}
//Map from Cello Part Type to SO term
function getPartType(part) {
if (part === 'ribozyme') {
return so + 'SO:0000374';
}
else if (part === 'scar') {
return so + 'SO:0001953';
}
else if (part === 'cds') {
return so + 'SO:0000316';
}
else if (part === 'promoter') {
return so + 'SO:0000167';
}
else if (part === 'rbs') {
return so + 'SO:0000139';
}
else if (part === 'terminator') {
return so + 'SO:0000141';
} else {
console.log('Part Type not found');
}
}