From 45c5aa64db4e885152a7e877878a25f1baeb20da Mon Sep 17 00:00:00 2001 From: haeussma <83341109+haeussma@users.noreply.github.com> Date: Wed, 6 Mar 2024 10:26:38 +0100 Subject: [PATCH] removed refs --- specifications/enzymeml.md | 78 +++++++++++++++++++------------------- 1 file changed, 39 insertions(+), 39 deletions(-) diff --git a/specifications/enzymeml.md b/specifications/enzymeml.md index 6aad8fa..0915f69 100644 --- a/specifications/enzymeml.md +++ b/specifications/enzymeml.md @@ -27,41 +27,41 @@ This is the root object that composes all objects found in an EnzymeML document. - Type: datetime - Description: Date the EnzymeML document was modified. - creators - - Type: [Creator](#creator) + - Type: Creator - Multiple: True - Description: Contains all authors that are part of the experiment. - vessels - - Type: [Vessel](#vessel) + - Type: Vessel - Multiple: True - Description: Contains all vessels that are part of the experiment. - proteins - - Type: [Protein](#Protein) + - Type: Protein - Multiple: True - Description: Contains all proteins that are part of the experiment. - complexes - - Type: [Complex](#Complex) + - Type: Complex - Multiple: True - Description: Contains all complexes that are part of the experiment. - reactants - - Type: [Reactant](#Reactant) + - Type: Reactant - Multiple: True - Description: Contains all reactants that are part of the experiment. - reactions - - Type: [Reaction](#reaction) + - Type: Reaction - Multiple: True - - Description: Dictionary mapping from reaction IDs to reaction describing objects. + - Description: Dictionary mapping from reaction IDs to reaction-describing objects. - measurements - - Type: [Measurement](#measurement) + - Type: Measurement - Multiple: True - Description: Contains measurements that describe outcomes of an experiment. - files - - Type: [File](#file) + - Type: File - Multiple: True - Description: Contains files attached to the data model. - global_parameters - - Type: [KineticParameter](#kineticparameter) + - Type: KineticParameter - Multiple: True - - Description: Dictionary mapping from parameter IDs to global kinetic parameter describing objects. + - Description: Dictionary mapping from parameter IDs to global kinetic parameters describing objects. ## General information @@ -116,7 +116,7 @@ This object is used to inherit basic attributes common to all species used in th - Type: string - Description: None - __vessel_id__ - - Type: @Vessel.id + - Type: string - Description: None - init_conc - Type: float @@ -159,7 +159,7 @@ This objects describes the proteins that were used or produced in the course of - Description: Unique identifier referencing a protein entry at UniProt. Use this identifier to initialize the object from the UniProt database. - Template_alias: UniProt ID - __ontology__ - - Type: [SBOTerm](#sboterm) + - Type: SBOTerm - Description: None - Default: SBOTerm.PROTEIN @@ -172,13 +172,13 @@ This object describes complexes made of reactants and/or proteins that were used - Multiple: True - Description: Array of IDs the complex contains - __ontology__ - - Type: [SBOTerm](#sboterm) + - Type: SBOTerm - Description: None - Default: SBOTerm.MACROMOLECULAR_COMPLEX ### Reactant [_AbstractSpecies_] -This objects describes the reactants that were used or produced in the course of the experiment. +This object describes the reactants that were used or produced in the course of the experiment. - smiles - Type: string @@ -192,8 +192,8 @@ This objects describes the reactants that were used or produced in the course of - Type: string - Description: Unique identifier of the CHEBI database. Use this identifier to initialize the object from the CHEBI database. - __ontology__ - - Type: [SBOTerm](#sboterm) - - Description: None + - Type: SBOTerm + - Description: SBO term defining the role of the given species in the reaction. - Default: SBOTerm.SMALL_MOLECULE ## EnzymeReaction @@ -227,7 +227,7 @@ This object describes a chemical or enzymatic reaction that was investigated in - Inclusiveminimum: 0 - Inclusivemaximum: 14 - __ontology__ - - Type: [SBOTerm](#sboterm) + - Type: SBOTerm - Default: SBOTerm.BIOCHEMICAL_REACTION - Description: Ontology defining the role of the given species. - uri @@ -237,30 +237,30 @@ This object describes a chemical or enzymatic reaction that was investigated in - Type: string - Description: Unique identifier of the author. - model - - Type: [KineticModel](#kineticmodel) - - Description: Kinetic model decribing the reaction. + - Type: KineticModel + - Description: Kinetic model describing the reaction. - educts - - Type: [ReactionElement](#reactionelement) + - Type: ReactionElement - Multiple: True - Description: List of educts containing ReactionElement objects. - Template_alias: Educts - products - - Type: [ReactionElement](#reactionelement) + - Type: ReactionElement - Multiple: True - Description: List of products containing ReactionElement objects. - Template_alias: Products - modifiers - - Type: [ReactionElement](#reactionelement) + - Type: ReactionElement - Multiple: True - - Description: List of modifiers (Proteins, snhibitors, stimulators) containing ReactionElement objects. + - Description: List of modifiers (proteins, inhibitors, stimulators) containing ReactionElement objects. - Template_alias: Modifiers ### ReactionElement -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. +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. - __species_id__ - - Type: @AbstractSpecies.id + - Type: string - Description: Internal identifier to either a protein or reactant defined in the EnzymeMLDocument. - References: EnzymeMLDocument.reactants.id - __stoichiometry__ @@ -272,7 +272,7 @@ This object is part of the Reaction object and describes either an educt, produc - Description: Whether or not the concentration of this species remains constant. - Default: False - ontology - - Type: [SBOTerm](#sboterm) + - Type: SBOTerm - Description: Ontology defining the role of the given species. ## Modelling @@ -288,11 +288,11 @@ This object describes a kinetic model that was derived from the experiment. - Type: string - Description: Equation for the kinetic law. - parameters - - Type: [KineticParameter](#kineticparameter) + - Type: KineticParameter - Multiple: True - Description: List of estimated parameters. - ontology - - Type: [SBOTerm](#sboterm) + - Type: SBOTerm - Description: Type of the estimated parameter. ### KineticParameter @@ -319,7 +319,7 @@ This object describes the parameters of the kinetic model and can include all es - Description: Lower bound of the estimated parameter. - __is_global__ - Type: bool - - Description: Specifies if this parameter is a global parameter. + - Description: Specifies if this parameter is global for the entire EnzymeMLDocument. - Default: False - stdev - Type: float @@ -329,7 +329,7 @@ This object describes the parameters of the kinetic model and can include all es - Description: Specifies if this parameter is constant - Default: False - ontology - - Type: [SBOTerm](#sboterm) + - Type: SBOTerm - Description: Type of the estimated parameter. ## Time course data handling @@ -355,7 +355,7 @@ This object describes the result of a measurement, which includes time course da - Inclusiveminimum: 0 - Inclusivemaximum: 14 - species - - Type: [MeasurementData](#measurementdata) + - Type: MeasurementData - Multiple: True - Description: Species of the measurement. - __global_time__ @@ -374,22 +374,22 @@ This object describes the result of a measurement, which includes time course da ### MeasurementData -This object describes a single entity of a measurement, which corresponds to one species. It also holds replicates which contain time course data. +This object describes a single entity of a measurement, which corresponds to one species. It also holds replicates that contain time course data. - __init_conc__ - Type: float - Description: Initial concentration of the measurement data. - __unit__ - Type: string - - Description: The unit of the measurement data. + - Description: The unit of measurement data. - __measurement_id__ - Type: string - Description: Unique measurement identifier this dataset belongs to. - species_id - - Type: @AbstractSpecies.id + - Type: string - Description: The identifier for the described reactant. - replicates - - Type: [Replicate](#replicate) + - Type: Replicate - Multiple: True - Description: A list of replicate objects holding raw data of the measurement. @@ -404,7 +404,7 @@ This object contains the measured time course data as well as metadata to the re - Type: string - Description: Unique identifier of the measurement that the replicate is part of. - __data_type__ - - Type: [DataTypes](#datatypes) + - Type: DataTypes - Description: Type of data that was measured (e.g. concentration) - Default: DataTypes.CONCENTRATION - __data_unit__ @@ -436,7 +436,7 @@ This object contains the measured time course data as well as metadata to the re ### File -This objects contains a files that has been attached to the document. +This object contains files that have been attached to the document. - __name__ - Type: string @@ -446,7 +446,7 @@ This objects contains a files that has been attached to the document. - Description: Contents of the file - __filetype__ - Type: string - - Description: Type of the file such as .xml, .json and so on + - Description: Type of the file such as .xml, .json, and so on ## Enumerations