{
"title": "EnzymeMLDocument",
"description": "This is the root object that composes all objects found in an EnzymeML document. It also includes general metadata such as the name of the document, when it was created/modified and references to publications, databases and arbitrary links to the web.",
"type": "object",
"properties": {
"id": {
"title": "Id",
"description": "Unique identifier of the given object.",
"xml": "@id",
"type": "string"
},
"name": {
"title": "Name",
"description": "Title of the EnzymeML Document.",
"type": "string"
},
"pubmedid": {
"title": "Pubmedid",
"description": "Pubmed ID reference.",
"type": "string"
},
"url": {
"title": "Url",
"description": "Arbitrary type of URL that is related to the EnzymeML document.",
"type": "string"
},
"doi": {
"title": "Doi",
"description": "Digital Object Identifier of the referenced publication or the EnzymeML document.",
"type": "string"
},
"created": {
"title": "Created",
"description": "Date the EnzymeML document was created.",
"type": "string",
"format": "date-time"
},
"modified": {
"title": "Modified",
"description": "Date the EnzymeML document was modified.",
"type": "string",
"format": "date-time"
},
"creators": {
"title": "Creators",
"description": "Contains all authors that are part of the experiment.",
"multiple": true,
"type": "array",
"items": {
"$ref": "#/definitions/Creator"
}
},
"vessels": {
"title": "Vessels",
"description": "Contains all vessels that are part of the experiment.",
"multiple": true,
"type": "array",
"items": {
"$ref": "#/definitions/Vessel"
}
},
"proteins": {
"title": "Proteins",
"description": "Contains all proteins that are part of the experiment.",
"multiple": true,
"type": "array",
"items": {
"$ref": "#/definitions/Protein"
}
},
"complexes": {
"title": "Complexes",
"description": "Contains all complexes that are part of the experiment.",
"multiple": true,
"type": "array",
"items": {
"$ref": "#/definitions/Complex"
}
},
"reactants": {
"title": "Reactants",
"description": "Contains all reactants that are part of the experiment.",
"multiple": true,
"type": "array",
"items": {
"$ref": "#/definitions/Reactant"
}
},
"reactions": {
"title": "Reactions",
"description": "Dictionary mapping from reaction IDs to reaction describing objects.",
"multiple": true,
"type": "array",
"items": {
"$ref": "#/definitions/Reaction"
}
},
"measurements": {
"title": "Measurements",
"description": "Contains measurements that describe outcomes of an experiment.",
"multiple": true,
"type": "array",
"items": {
"$ref": "#/definitions/Measurement"
}
},
"files": {
"title": "Files",
"description": "Contains files attached to the data model.",
"multiple": true,
"type": "array",
"items": {
"$ref": "#/definitions/File"
}
},
"global_parameters": {
"title": "Global Parameters",
"description": "Dictionary mapping from parameter IDs to global kinetic parameter describing objects.",
"multiple": true,
"type": "array",
"items": {
"$ref": "#/definitions/KineticParameter"
}
}
},
"required": [
"name"
],
"definitions": {
"Creator": {
"title": "Creator",
"description": "The creator object contains all information about authors that contributed to the resulting document.",
"type": "object",
"properties": {
"id": {
"title": "Id",
"description": "Unique identifier of the given object.",
"xml": "@id",
"type": "string"
},
"given_name": {
"title": "Given Name",
"description": "Given name of the author or contributor.",
"type": "string"
},
"family_name": {
"title": "Family Name",
"description": "Family name of the author or contributor.",
"type": "string"
},
"mail": {
"title": "Mail",
"description": "Email address of the author or contributor.",
"type": "string"
}
},
"required": [
"given_name",
"family_name",
"mail"
]
},
"Vessel": {
"title": "Vessel",
"description": "This object describes vessels in which the experiment has been carried out. These can include any type of vessel used in biocatalytic experiments.",
"type": "object",
"properties": {
"id": {
"title": "Id",
"description": "Unique identifier of the given object.",
"xml": "@id",
"type": "string"
},
"name": {
"title": "Name",
"description": "Name of the used vessel.",
"template_alias": "Name",
"type": "string"
},
"volume": {
"title": "Volume",
"description": "Volumetric value of the vessel.",
"template_alias": "Volume value",
"exclusiveMinimum": 0,
"type": "number"
},
"unit": {
"title": "Unit",
"description": "Volumetric unit of the vessel.",
"template_alias": "Volume unit",
"type": "string"
},
"constant": {
"title": "Constant",
"description": "Whether the volume of the vessel is constant or not.",
"default": true,
"type": "boolean"
},
"uri": {
"title": "Uri",
"description": "URI of the vessel.",
"type": "string"
},
"creator_id": {
"title": "Creator Id",
"description": "Unique identifier of the author.",
"type": "string"
}
},
"required": [
"name",
"volume",
"unit"
]
},
"SBOTerm": {
"title": "SBOTerm",
"type": "string",
"description": "An enumeration.",
"enum": [
"SBO:0000176",
"SBO:0000208",
"SBO:0000181",
"SBO:0000182",
"SBO:0000179",
"SBO:0000180",
"SBO:0000209",
"SBO:0000377",
"SBO:0000177",
"SBO:0000200",
"SBO:0000672",
"SBO:0000252",
"SBO:0000251",
"SBO:0000247",
"SBO:0000327",
"SBO:0000328",
"SBO:0000336",
"SBO:0000015",
"SBO:0000011",
"SBO:0000013",
"SBO:0000020",
"SBO:0000461",
"SBO:0000462",
"SBO:0000021",
"SBO:0000296",
"SBO:0000297",
"SBO:0000607",
"SBO:0000028",
"SBO:0000025",
"SBO:0000027",
"SBO:0000186"
]
},
"Protein": {
"title": "Protein",
"description": "This objects describes the proteins that were used or produced in the course of the experiment.",
"type": "object",
"properties": {
"id": {
"title": "Id",
"description": "Unique identifier of the given object.",
"xml": "@id",
"type": "string"
},
"name": {
"title": "Name",
"description": "None",
"type": "string"
},
"vessel_id": {
"title": "Vessel Id",
"description": "None",
"type": "string"
},
"init_conc": {
"title": "Init Conc",
"description": "None",
"type": "number"
},
"constant": {
"title": "Constant",
"description": "None",
"type": "boolean"
},
"unit": {
"title": "Unit",
"description": "None",
"type": "string"
},
"uri": {
"title": "Uri",
"description": "None",
"type": "string"
},
"creator_id": {
"title": "Creator Id",
"description": "None",
"type": "string"
},
"sequence": {
"title": "Sequence",
"description": "Amino acid sequence of the protein",
"template_alias": "Sequence",
"type": "string"
},
"ecnumber": {
"title": "Ecnumber",
"description": "EC number of the protein.",
"pattern": "(\\d+.)(\\d+.)(\\d+.)(\\d+)",
"template_alias": "EC Number",
"type": "string"
},
"organism": {
"title": "Organism",
"description": "Organism the protein was expressed in.",
"template_alias": "Source organism",
"type": "string"
},
"organism_tax_id": {
"title": "Organism Tax Id",
"description": "Taxonomy identifier of the expression host.",
"type": "string"
},
"uniprotid": {
"title": "Uniprotid",
"description": "Unique identifier referencing a protein entry at UniProt. Use this identifier to initialize the object from the UniProt database.",
"template_alias": "UniProt ID",
"type": "string"
},
"ontology": {
"description": "None",
"default": "SBO:0000013",
"allOf": [
{
"$ref": "#/definitions/SBOTerm"
}
]
}
},
"required": [
"name",
"vessel_id",
"constant",
"sequence"
]
},
"Complex": {
"title": "Complex",
"description": "This object describes complexes made of reactants and/or proteins that were used or produced in the course of the experiment.",
"type": "object",
"properties": {
"id": {
"title": "Id",
"description": "Unique identifier of the given object.",
"xml": "@id",
"type": "string"
},
"name": {
"title": "Name",
"description": "None",
"type": "string"
},
"vessel_id": {
"title": "Vessel Id",
"description": "None",
"type": "string"
},
"init_conc": {
"title": "Init Conc",
"description": "None",
"type": "number"
},
"constant": {
"title": "Constant",
"description": "None",
"type": "boolean"
},
"unit": {
"title": "Unit",
"description": "None",
"type": "string"
},
"uri": {
"title": "Uri",
"description": "None",
"type": "string"
},
"creator_id": {
"title": "Creator Id",
"description": "None",
"type": "string"
},
"participants": {
"title": "Participants",
"description": "Array of IDs the complex contains",
"pattern": "[s|p][\\d]+",
"multiple": true,
"type": "array",
"items": {
"type": "string",
"pattern": "[s|p][\\d]+"
}
},
"ontology": {
"description": "None",
"default": "SBO:0000296",
"allOf": [
{
"$ref": "#/definitions/SBOTerm"
}
]
}
},
"required": [
"name",
"vessel_id",
"constant"
]
},
"Reactant": {
"title": "Reactant",
"description": "This objects describes the reactants that were used or produced in the course of the experiment.",
"type": "object",
"properties": {
"id": {
"title": "Id",
"description": "Unique identifier of the given object.",
"xml": "@id",
"type": "string"
},
"name": {
"title": "Name",
"description": "None",
"type": "string"
},
"vessel_id": {
"title": "Vessel Id",
"description": "None",
"type": "string"
},
"init_conc": {
"title": "Init Conc",
"description": "None",
"type": "number"
},
"constant": {
"title": "Constant",
"description": "None",
"type": "boolean"
},
"unit": {
"title": "Unit",
"description": "None",
"type": "string"
},
"uri": {
"title": "Uri",
"description": "None",
"type": "string"
},
"creator_id": {
"title": "Creator Id",
"description": "None",
"type": "string"
},
"smiles": {
"title": "Smiles",
"description": "Simplified Molecular Input Line Entry System (SMILES) encoding of the reactant.",
"template_alias": "SMILES",
"type": "string"
},
"inchi": {
"title": "Inchi",
"description": "International Chemical Identifier (InChI) encoding of the reactant.",
"template_alias": "InCHI",
"type": "string"
},
"chebi_id": {
"title": "Chebi Id",
"description": "Unique identifier of the CHEBI database. Use this identifier to initialize the object from the CHEBI database.",
"type": "string"
},
"ontology": {
"description": "None",
"default": "SBO:0000247",
"allOf": [
{
"$ref": "#/definitions/SBOTerm"
}
]
}
},
"required": [
"name",
"vessel_id",
"constant"
]
},
"KineticParameter": {
"title": "KineticParameter",
"description": "This object describes the parameters of the kinetic model and can include all estimated values.",
"type": "object",
"properties": {
"id": {
"title": "Id",
"description": "Unique identifier of the given object.",
"xml": "@id",
"type": "string"
},
"name": {
"title": "Name",
"description": "Name of the estimated parameter.",
"type": "string"
},
"value": {
"title": "Value",
"description": "Numerical value of the estimated parameter.",
"type": "number"
},
"unit": {
"title": "Unit",
"description": "Unit of the estimated parameter.",
"type": "string"
},
"initial_value": {
"title": "Initial Value",
"description": "Initial value that was used for the parameter estimation.",
"type": "number"
},
"upper": {
"title": "Upper",
"description": "Upper bound of the estimated parameter.",
"type": "number"
},
"lower": {
"title": "Lower",
"description": "Lower bound of the estimated parameter.",
"type": "number"
},
"is_global": {
"title": "Is Global",
"description": "Specifies if this parameter is a global parameter.",
"default": false,
"type": "boolean"
},
"stdev": {
"title": "Stdev",
"description": "Standard deviation of the estimated parameter.",
"type": "number"
},
"constant": {
"title": "Constant",
"description": "Specifies if this parameter is constant",
"default": false,
"type": "boolean"
},
"ontology": {
"description": "Type of the estimated parameter.",
"allOf": [
{
"$ref": "#/definitions/SBOTerm"
}
]
}
},
"required": [
"name",
"value",
"unit"
]
},
"KineticModel": {
"title": "KineticModel",
"description": "This object describes a kinetic model that was derived from the experiment.",
"type": "object",
"properties": {
"id": {
"title": "Id",
"description": "Unique identifier of the given object.",
"xml": "@id",
"type": "string"
},
"name": {
"title": "Name",
"description": "Name of the kinetic law.",
"type": "string"
},
"equation": {
"title": "Equation",
"description": "Equation for the kinetic law.",
"type": "string"
},
"parameters": {
"title": "Parameters",
"description": "List of estimated parameters.",
"multiple": true,
"type": "array",
"items": {
"$ref": "#/definitions/KineticParameter"
}
},
"ontology": {
"description": "Type of the estimated parameter.",
"allOf": [
{
"$ref": "#/definitions/SBOTerm"
}
]
}
},
"required": [
"name",
"equation"
]
},
"ReactionElement": {
"title": "ReactionElement",
"description": "This object is part of the Reaction object and describes either an educt, product or modifier. The latter includes buffers, counter-ions as well as proteins/enzymes.",
"type": "object",
"properties": {
"id": {
"title": "Id",
"description": "Unique identifier of the given object.",
"xml": "@id",
"type": "string"
},
"species_id": {
"title": "Species Id",
"description": "Internal identifier to either a protein or reactant defined in the EnzymeMLDocument.",
"type": "string"
},
"stoichiometry": {
"title": "Stoichiometry",
"description": "Positive float number representing the associated stoichiometry.",
"default": 1,
"exclusiveMinimum": 0,
"type": "number"
},
"constant": {
"title": "Constant",
"description": "Whether or not the concentration of this species remains constant.",
"default": false,
"type": "boolean"
},
"ontology": {
"description": "Ontology defining the role of the given species.",
"allOf": [
{
"$ref": "#/definitions/SBOTerm"
}
]
}
},
"required": [
"species_id"
]
},
"Reaction": {
"title": "Reaction",
"description": "This object describes a chemical or enzymatic reaction that was investigated in the course of the experiment. All species used within this object need to be part of the data model.",
"type": "object",
"properties": {
"id": {
"title": "Id",
"description": "Unique identifier of the given object.",
"xml": "@id",
"type": "string"
},
"name": {
"title": "Name",
"description": "Name of the reaction.",
"template_alias": "Name",
"type": "string"
},
"reversible": {
"title": "Reversible",
"description": "Whether the reaction is reversible or irreversible",
"default": false,
"template_alias": "Reversible",
"type": "boolean"
},
"temperature": {
"title": "Temperature",
"description": "Numeric value of the temperature of the reaction.",
"template_alias": "Temperature value",
"type": "number"
},
"temperature_unit": {
"title": "Temperature Unit",
"description": "Unit of the temperature of the reaction.",
"pattern": "kelvin|Kelvin|k|K|celsius|Celsius|C|c",
"template_alias": "Temperature unit",
"type": "string"
},
"ph": {
"title": "Ph",
"description": "PH value of the reaction.",
"template_alias": "pH value",
"inclusiveminimum": 0,
"inclusivemaximum": 14,
"type": "number"
},
"ontology": {
"description": "Ontology defining the role of the given species.",
"default": "SBO:0000176",
"allOf": [
{
"$ref": "#/definitions/SBOTerm"
}
]
},
"uri": {
"title": "Uri",
"description": "URI of the reaction.",
"type": "string"
},
"creator_id": {
"title": "Creator Id",
"description": "Unique identifier of the author.",
"type": "string"
},
"model": {
"title": "Model",
"description": "Kinetic model decribing the reaction.",
"allOf": [
{
"$ref": "#/definitions/KineticModel"
}
]
},
"educts": {
"title": "Educts",
"description": "List of educts containing ReactionElement objects.",
"multiple": true,
"template_alias": "Educts",
"type": "array",
"items": {
"$ref": "#/definitions/ReactionElement"
}
},
"products": {
"title": "Products",
"description": "List of products containing ReactionElement objects.",
"multiple": true,
"template_alias": "Products",
"type": "array",
"items": {
"$ref": "#/definitions/ReactionElement"
}
},
"modifiers": {
"title": "Modifiers",
"description": "List of modifiers (Proteins, snhibitors, stimulators) containing ReactionElement objects.",
"multiple": true,
"template_alias": "Modifiers",
"type": "array",
"items": {
"$ref": "#/definitions/ReactionElement"
}
}
},
"required": [
"name"
]
},
"DataTypes": {
"title": "DataTypes",
"description": "An enumeration.",
"enum": [
"conc",
"abs",
"feed",
"biomass",
"conversion",
"peak-area"
]
},
"Replicate": {
"title": "Replicate",
"description": "This object contains the measured time course data as well as metadata to the replicate itself.",
"type": "object",
"properties": {
"id": {
"title": "Id",
"description": "Unique identifier of the given object.",
"xml": "@id",
"type": "string"
},
"species_id": {
"title": "Species Id",
"description": "Unique identifier of the species that has been measured.",
"type": "string"
},
"measurement_id": {
"title": "Measurement Id",
"description": "Unique identifier of the measurement that the replicate is part of.",
"type": "string"
},
"data_type": {
"description": "Type of data that was measured (e.g. concentration)",
"default": "conc",
"allOf": [
{
"$ref": "#/definitions/DataTypes"
}
]
},
"data_unit": {
"title": "Data Unit",
"description": "SI unit of the data that was measured.",
"type": "string"
},
"time_unit": {
"title": "Time Unit",
"description": "Time unit of the replicate.",
"type": "string"
},
"time": {
"title": "Time",
"description": "Time steps of the replicate.",
"multiple": true,
"type": "array",
"items": {
"type": "number"
}
},
"data": {
"title": "Data",
"description": "Data that was measured.",
"multiple": true,
"type": "array",
"items": {
"type": "number"
}
},
"is_calculated": {
"title": "Is Calculated",
"description": "Whether or not the data has been generated by simulation.",
"default": false,
"type": "boolean"
},
"uri": {
"title": "Uri",
"description": "URI of the protein.",
"type": "string"
},
"creator_id": {
"title": "Creator Id",
"description": "Unique identifier of the author.",
"type": "string"
}
},
"required": [
"species_id",
"measurement_id",
"data_unit",
"time_unit"
]
},
"MeasurementData": {
"title": "MeasurementData",
"description": "This object describes a single entity of a measurement, which corresponds to one species. It also holds replicates which contain time course data.",
"type": "object",
"properties": {
"id": {
"title": "Id",
"description": "Unique identifier of the given object.",
"xml": "@id",
"type": "string"
},
"init_conc": {
"title": "Init Conc",
"description": "Initial concentration of the measurement data.",
"type": "number"
},
"unit": {
"title": "Unit",
"description": "The unit of the measurement data.",
"type": "string"
},
"measurement_id": {
"title": "Measurement Id",
"description": "Unique measurement identifier this dataset belongs to.",
"type": "string"
},
"species_id": {
"title": "Species Id",
"description": "The identifier for the described reactant.",
"type": "string"
},
"replicates": {
"title": "Replicates",
"description": "A list of replicate objects holding raw data of the measurement.",
"multiple": true,
"type": "array",
"items": {
"$ref": "#/definitions/Replicate"
}
}
},
"required": [
"init_conc",
"unit",
"measurement_id"
]
},
"Measurement": {
"title": "Measurement",
"description": "This object describes the result of a measurement, which includes time course data of any type defined in DataTypes. It includes initial concentrations of all species used in a single measurement.",
"type": "object",
"properties": {
"id": {
"title": "Id",
"description": "Unique identifier of the given object.",
"xml": "@id",
"type": "string"
},
"name": {
"title": "Name",
"description": "Name of the measurement",
"type": "string"
},
"temperature": {
"title": "Temperature",
"description": "Numeric value of the temperature of the reaction.",
"template_alias": "Temperature value",
"type": "number"
},
"temperature_unit": {
"title": "Temperature Unit",
"description": "Unit of the temperature of the reaction.",
"pattern": "kelvin|Kelvin|k|K|celsius|Celsius|C|c",
"type": "string"
},
"ph": {
"title": "Ph",
"description": "PH value of the reaction.",
"inclusiveminimum": 0,
"inclusivemaximum": 14,
"type": "number"
},
"species": {
"title": "Species",
"description": "Species of the measurement.",
"multiple": true,
"type": "array",
"items": {
"$ref": "#/definitions/MeasurementData"
}
},
"global_time": {
"title": "Global Time",
"description": "Global time of the measurement all replicates agree on.",
"multiple": true,
"type": "array",
"items": {
"type": "number"
}
},
"global_time_unit": {
"title": "Global Time Unit",
"description": "Unit of the global time.",
"type": "string"
},
"uri": {
"title": "Uri",
"description": "URI of the reaction.",
"type": "string"
},
"creator_id": {
"title": "Creator Id",
"description": "Unique identifier of the author.",
"type": "string"
}
},
"required": [
"name",
"temperature",
"temperature_unit",
"ph",
"global_time_unit"
]
},
"File": {
"title": "File",
"description": "This objects contains a files that has been attached to the document.",
"type": "object",
"properties": {
"id": {
"title": "Id",
"description": "Unique identifier of the given object.",
"xml": "@id",
"type": "string"
},
"name": {
"title": "Name",
"description": "Name of the file",
"type": "string"
},
"content": {
"title": "Content",
"description": "Contents of the file",
"type": "string",
"format": "binary"
},
"filetype": {
"title": "Filetype",
"description": "Type of the file such as .xml, .json and so on",
"type": "string"
}
},
"required": [
"name",
"content",
"filetype"
]
}
}
}