biosim-schema

Schema for Biomolecular Simulation Data

URI: https://CCPBioSim.ac.uk/biosim-schema/

Name: biosim-schema

Classes

Class	Description
Analysis	Analysis stage of simulation workflow
AngleQuantity	A quantity representing angles
Barostat	Settings used for the simulation barostat
ByteQuantity	A quantity representing bytes
CarbohydratePotential	Potential used for carbohydrate molecules
ChargeQuantity	A quantity representing charge
CompressibilityQuantity	A quantity representing compressibility
ComputationalEnvironment	Computational environment used to perform simulation
ConcentrationQuantity	A quantity representing concentration
Connectivity	Connectivity information included in the topology
EnergyQuantity	A quantity representing energy
Ensemble	Simulation ensemble/thermodynamic properties
Equilibration	Equilibration stage of simulation workflow
ForceQuantity	A quantity representing force
FrequencyQuantity	A quantity representing frequency
FrictionCoefficientQuantity	A quantity representing friction coefficients
GeneralPotential	Potential used for molecules
Hardware	Computer hardware used to perform simulation
Integrator	Settings used for the simulation integrator
Interactions	Settings used to define particle interactions
LengthQuantity	A quantity representing length
LipidPotential	Potential used for lipid molecules
MachineLearnedPotential	Machine learned potential used for molecules
MassQuantity	A quantity representing mass
MatrixCompressibilityQuantity	A quantity representing compressibility vectors in 3D
MatrixPressureQuantity	A quantity representing pressure vectors in 3D
MatrixQuantity	A quantity representing general vectors in 3D
Minimisation	Minimisation stage of simulation workflow
MolarEnergyQuantity	A quantity representing molar energy
MoleculeID	Identifiers of a molecule type in the simulated system
NucleicPotential	Potential used for nucleic acid molecules
Particles	Particle information included in the topology
Performance	Compute performance during simulation
PolymerPotential	Potential used for polymers molecules
PotentialMetadata	Potentials used for various modelled molecules
PressureQuantity	A quantity representing pressure
Production	Production stage of simulation workflow
ProteinPotential	Potential used for protein molecules
Setup	Setup stage of simulation workflow
SimulationAverages	Average values of observables outputted from the simulation
SimulationBox	Simulation box information
SimulationMetadata	root class for biosim-schema
SimulationObservables	Simulation observables outputted from simulation
SimulationSettings	Settings in simulation
SimulationStages	Stages of simulation workflow
Software	Computer software used to perform simulation
SystemComposition	Molecular composition of simulated system
SystemCounts	Entity counts across the simulated system
TemperatureQuantity	A quantity representing temperature
Thermostat	Settings used for the simulation thermostat
TimeQuantity	A quantity representing time
TopologyMetadata	Topology information
Trajectories	Information in trajectory files
TrajectoryMetadata	Trajectory information
VectorAngleQuantity	A quantity representing 3D angles
VectorCompressibilityQuantity	A quantity representing compressibility in 3D
VectorLengthQuantity	A quantity representing 3D lengths/dimensions
VectorPressureQuantity	A quantity representing pressure in 3D
VectorTemperatureQuantity	Temperature values for multiple coupling groups
VectorTimeQuantity	Time values for multiple coupling groups
VectorVolumeQuantity	A quantity representing volume as via 3 length dimensions
VolumeQuantity	A quantity representing volume
WaterPotential	Potential used for water molecules

Slots

Slot	Description
alphafold_ID	AlphaFold predicted protein structure identifier (AlphaFold DB, EMBL-EBI)
analysis	Analysis stage of a simulation
analysis_method	Name of the method used to analyse simulation
analysis_software	Name of software used to analyse simulation
analysis_tool	Name of the tool used to analyse simulation
atom_count	Number of atoms in a molecule
average_enthalpy	Average enthalpy sampled from the simulation, given as a float
average_kinetic_energy	Average kinetic energy sampled from the simulation, given as a float
average_potential_energy	Average potential energy sampled from the simulation, given as a float
average_pressure	Average pressure sampled from the simulation, given as a float
average_temperature	Average temperature sampled from the simulation, given as a float
average_volume	Average volume sampled from the simulation, given as a float
average_volume_vector	Average volume sampled from the simulation, given as a list, (e
barostat	Barostat information
barostat_algorithm	List of barostat algorithms used in the simulation
bond_length_constraints_algorithm	Constraints applied to bonds between two particles in the simulated system
bonds	Are bond parameters present in the topology?
box_angles	The angles of the box used to simulate the system
box_dimensions	The lengths/dimensions of the box used to simulate the system
box_type	The type of box used to simuluate the system
carbohydrate_potential	Force field for carbohydrates
carbohydrate_potential_name	Force field used to describe carbohydrate
chain_length	Usually required in the Nosé-Hoover thermostat, the chain length (e
coarse_grained	Are atoms coarse-grained?
collision_frequency	Collision frequency for the integrator, given as a float
composition	Composition of simulated system
compressibility	Compressibility of the simulated system, given as a float
compressibility_vector	Compressibility of the simulated system, given as a float
compute	Computational environment information
connectivity	Particle connectivity information
container_runtime	Container runtime used to execute the simulation environment, if any
cores_per_socket	Number of physical CPU cores in each socket
coupling_group	A subset of atoms for which temperature is controlled, often needed for simul…
CPU_architecture	CPU instruction-set architecture of the compute nodes
CPU_vendor	CPU vendor used in the compute nodes
dihedrals	Are dihedral parameters present in the topology?
electrostatic_cutoff_distance	Distance in Angstrom at which a electrostatic interaction is turned off and a…
EMDB_ID	Electron Microscopy Data Bank ID
energies	Are per-frame energies included in the trajectory?
energy_consumption	Total energy consumed by the simulation run
energy_tolerance	Tolerance energy for when minimization stops, this is when the maximum force …
engine_mapping	Mapping from engine-specific parameter names to schema slots
ensemble	Ensemble information
ensemble_type	List of ensemble types used in the simulation
equilibration	Equilibration stage of a simulation
execution_platform	Broad type of system used to run the simulation workload
fixed_charges	Are fixed charges on atoms included in the topology?
forces	Are per-frame forces included in the trajectory?
frame_count	Total number of snapshots that make up a trajectory
frame_step	Time between saved snapshots/frames in a simulation, given as a float
friction_coefficient	Usually used in the Langevin thermostat, the friction coefficient determines …
general_potential	Force field for molecules (in general)
general_potential_name	Force field used to describe molecules
GPU_vendor	GPU vendor used by the compute nodes, if applicable
GPUs_per_node	Number of GPUs present in each compute node
hardware	Computer hardware used to perform simulation
identifier	External database identifier
InChI	The International Chemical Identifier (InChi) is a textual identifier for che…
InChIKey	The condensed, 27 character InChIKey, which is a hashed version of the full I…
integrator	Integrator information
integrator_algorithm	List of integrator algorithms used to integrate the simulation
interactions	Interaction information
lipid_potential	Force field for lipids
lipid_potential_name	Force field used to describe lipids
long_range_interaction_method	Method used to describe long-range interactions between particles
machine_learned_potential	ML force field for molecules (in general)
machine_learned_potential_name	ML force field used to describe molecules
masses	Are masses present in the topology?
memory_per_node	Amount of memory installed per compute node
minimisation	Minimisation stage of a simulation
minimisation_algorithm	Name of the method used to minimise the molecular system
minimisation_distance_step_size	The distance the algorithm moves in a single step, controls how large a step …
modified	Has the initial model been modified from the original?
molecular_formula	The molecular formula of a molecule\
molecular_weight	The molecular weight of a molecule
molecule_charge	Electrostatic charge of a molecule
molecule_count	Number of instances of a given molecule, defined as bonded atoms or beads
molecule_ID	Persistent identifier of a molecule being simulated
monomer_count	Number of monomeric units in a polymer(e
MPI_library	MPI implementation used for distributed parallel execution
node_count	Number of compute nodes used for the run
node_type	Compute node profile used for the simulation run
nucleic_potential	Force field for nucleic acids
nucleic_potential_name	Force field used to describe nucleic acids
nucleic_sequence	One letter sequence for nucleic acid nucleotides
number_of_minimisation_steps	Number of integration steps performed during minimisation of the system, give…
number_of_steps	Number of integration steps performed in the simulation, given as an integer
observables	Simulation observables
operating_system	Operating system installed on the hardware used to perform the simulation
particles	Particles information
PDB_ID	Protein Data Bank identifier
performance	Compute performance during simulation
periodic_boundary_conditions	What directions in a simulation cell periodic boundaries are set if they are …
polarizable_charges	Are per-frame polarizable charges included in the trajectory?
polymer_potential	Force field for polymers (excluding proteins and nucleic acids)
polymer_potential_name	Force field used to describe polymers (excluding proteins and nucleic acids)
positions	Are per-frame positions included in the trajectory?
potentials	Force field potentials used to describe simulated particles
predicted_structure	Are the molecule positions derived from a prediction?
pressure_coupling_frequency	Step frequency to apply the barostat, given as an integer
pressure_coupling_type	List of coupling types for adjusting box vectors
pressure_time_constant	Time constant/step (relaxation time of pressure) used for coupling the system…
production	Production stage of a simulation
protein_potential	Force field for proteins
protein_potential_name	Force field used to describe proteins
protein_sequence	One letter sequence for protein amino acids
PubChem_CID	PubChem CID of chemical molecules and their activities against biological ass…
random_seed	Random number used to set (a) distribution of velocities across particles at …
replica	Is this trajectory a replica of another provided trajectory?
resolution	Resolution of simulated system
restraints	Are any positional restraints applied to molecule dynamics? (Restraints usual…
salt_concentration	Concentration of salt in the solution
scheduler	Workload manager or job scheduler used to launch the simulation
settings	Simulation settings
setup	Setup stage of a simulation
setup_tool	Name of the tool used to setup simulation
simulation_averages	Average values of observables outputted from the simulation
simulation_box	Information about the simulation box
simulation_method	Method used to perform simulation
simulation_software	Name of software used to perform simulation step
simulation_software_version	Version of software used to perform simulation step
simulation_time	Total time molecular dynamics have been sampled in a simulation trajectory, o…
simulation_tool	Tool used to perform simulation
SMILES	Simplified Molecular Input Line Entry System (SMILES) ASCII-based line notati…
sockets_per_node	Number of physical CPU sockets in each compute node
software	Computer software used to perform simulation
stages	Simulation stages
system_charge	Total electrostatic charge of the system given by the elementary charge (e)
system_counts	Entity counts across the simulated system
target_pressure	Target/reference pressure set to reach in the simulation, given as a float
target_pressure_vector	Target/reference pressure set to reach in the simulation, given as a 3x3 arra…
target_temperature	Target/reference temperature set to reach in the simulation, given as a float
target_temperature_vector	Target/reference temperature set to reach in the simulation, given as a list …
temperature_time_constant	Time constant for coupling the system temperature in seconds units, given as …
thermostat	thermostat information
thermostat_algorithm	List of thermostat algorithms used in the simulation
threads_per_core	Number of hardware threads per physical core
time_step	Time between integration steps in a simulation, given as a float
topology	Topology information
total_atom_count	Total number of atoms in the simulation
total_molecule_count	Total number of simulated molecules, defined as bonded atoms or beads
trajectory	Trajectory information
trajectory_output	Information included in trajectory files
UNIPROT_ID	UniProt accession ID
unique_molecule_count	Number of unique simulated molecules, defined as bonded atoms or beads
value	value for a given quantity
value_unit	unit for a given value
vdw_cutoff_distance	Distance in Angstrom at which a Van der Waals interaction is turned off and a…
vector_value	vector value for a given quantity
velocities	Are per-frame velocities included in the trajectory?
wall_time	Total elapsed runtime of the simulation
water	Are water molecules included in the trajectory?
water_potential	Force field for water molecules
water_potential_name	Force field used to describe water molecules

Enumerations

Enumeration	Description
AnalysisMethod	Methods used to analyse simulation outputs
AnalysisSoftware	Software used to analyse simulation outputs
AnalysisTool	Tools used to analyse simulation outputs
AngleUnit	Units for angles
BarostatAlgorithm	Barostat algorithm used to set the pressure in a simulation
BondLengthConstraintsAlgorithm	Fix specific molecular degrees of freedom—typically fast bond vibrations invo…
BoxType	Types of box used to simulate the system
ByteUnit	Units for Bytes
CarbohydratePotentialName	Force fields used to parametrize carbohydrates in a simulation
ChargeUnit	Units for charge quantity
CompressibilityUnit	measures how the system volume responds to pressure changes
ConcentrationUnit	Units for concentration quantity
ContainerRuntime	Container runtime used to package and run software
CpuArchitecture	CPU architecture used by the compute nodes
CpuVendor	Vendor of the CPU used in the compute nodes
EnergyUnit	Units for energy
EnsembleType	Ensemble used in a simulation
ExecutionPlatform	Type of platform used to run the simulation
ForceUnit	Units for force
FrequencyUnit	Units used to describe frequency
FrictionCoefficientUnit	Relationship between applied forces and the resulting resistance to motion
GeneralPotentialName	Force fields used to parametrize molecules in a simulation
GpuVendor	Vendor of the GPU used in the compute nodes
IntegratorAlgorithm	Algorithm used to integrate the simulation
LengthUnit	Units for length quantity
LipidPotentialName	Force fields used to parametrize lipids in a simulation
LongRangeInteractionMethod	Method used to implement long-range interactions of point charges in the simu…
MachineLearnedPotentialName	Machine learned potentials
MassUnit	Units for mass/molecular weight
MinimisationAlgorithm	Algorithm used to minimise particle interactions
ModelResolution	Resolution of simulated molecules
MolarEnergyUnit	Units for molar energy
MPILibrary	MPI implementation used for message passing
NodeType	Type of compute node used in the system
NucleicPotentialName	Force fields used to parametrize nucleic acids in a simulation
OperatingSystem	List of operating systems installed on the hardware used to perform the simul…
PeriodicBoundaryConditions	What directions in a simulation cell periodic boundaries are set if they are …
PolymerPotentialName	Force fields used to parametrize polymers in a simulation
PressureCouplingType	Coupling type for adjusting box vectors
PressureUnit	Units to describe pressure
ProteinPotentialName	Force fields used to parametrize amino acids in proteins in a simulation
Scheduler	Job scheduler used for simulation execution
SetupTool	Tool used to setup a system for simulation
SimulationMethod	Options for simulation methods
SimulationSoftware	Simulation software used to perform molecular dynamics simulations and relate…
SimulationTool	Tools/utility used within simulation engines to perform simulations
TemperatureUnit	Units to describe temperature
ThermostatAlgorithm	Thermostat algorithm used to set the temperature in a simulation
TimeUnit	Units used to describe time
VolumeUnit	Units for volume quantity
WaterPotentialName	Force fields used to parametrize water molecules in a simulation

Types

Type	Description
boolean	A binary (true or false) value
curie	a compact URI
date	a date (year, month and day) in an idealized calendar
date_or_datetime	Either a date or a datetime
datetime	The combination of a date and time
decimal	A real number with arbitrary precision that conforms to the xsd:decimal speci…
double	A real number that conforms to the xsd:double specification
float	A real number that conforms to the xsd:float specification
integer	An integer
jsonpath	A string encoding a JSON Path
jsonpointer	A string encoding a JSON Pointer
ncname	Prefix part of CURIE
nodeidentifier	A URI, CURIE or BNODE that represents a node in a model
objectidentifier	A URI or CURIE that represents an object in the model
sparqlpath	A string encoding a SPARQL Property Path
string	A character string
time	A time object represents a (local) time of day, independent of any particular…
uri	a complete URI
uriorcurie	a URI or a CURIE

Subsets

Subset	Description