5.5 Documentation of Molecular Models
87
Fig. 5.7 Correspondences between the domain and top levels; example: Description of a materials
modelling use case following MODA [20] and OSMO [21]. Ellipses denote individuals, labelled by
the concept names from the respective ontologies (EVMPO, OSMO and multiple EMMO modules),
and arrows denote relations. At the intermediate stage, mereosemiotic chain relations from VIPRS
are used to support the alignment [42]
5.5 Documentation of Molecular Models
For documenting molecular models and exchanging them between platforms, a
semantic interoperability standard on the basis of the VIMMP system of ontologies as well as MODA [20] was agreed between VIMMP and the Molecular Model
Database (MolMod DB) of the Boltzmann-Zuse Society [43]; the associated environment of interoperable platforms will prospectively also include Bottled SAFT [44].
The structure of the knowledge graph representing a molecular model is illustrated by Fig. 5.8, which corresponds to a two-centre Lennard-Jones plus pointquadrupole model (2CLJQ) where a molecule (in this case, acetylene) is represented
by a rigid unit (viso-am:rigid_object), consisting of two Lennard-Jones interaction
sites (viso-am:lj_site), a point-quadrupole site (viso-am:charge_quadrupole_site) as
well as a viso-am:structureless_object, representing the molecular centre of mass,
which is used the initial point of vov:relative_position vectors that indicate the coordinates of the interaction sites. The relation vov:has_attached_variable and subproperties of it are used to connect the interaction sites with the non-geometrical model
parameters, i.e. the mass associated with each of the two LJ sites (half the molecular
mass), the σ and site and energy parameters of the LJ potential, and a secondorder tensor characterizing the quadrupole moment. Other rigid molecular models
are described analogously.
The platform interoperability implementation developed on this basis employs
JSON-LD to exchange information on molecular models. Therefore, the knowledge
graph needs to be connected (i.e. it may not consist of multiple connected components), and its topology needs to be simplified to a tree structure such that each object
is subordinate to exactly one object, except for a single root node at the top. For the
present example, an osmo:workflow_graph with two sections, a use case (MODA
87
Fig. 5.7 Correspondences between the domain and top levels; example: Description of a materials
modelling use case following MODA [20] and OSMO [21]. Ellipses denote individuals, labelled by
the concept names from the respective ontologies (EVMPO, OSMO and multiple EMMO modules),
and arrows denote relations. At the intermediate stage, mereosemiotic chain relations from VIPRS
are used to support the alignment [42]
5.5 Documentation of Molecular Models
For documenting molecular models and exchanging them between platforms, a
semantic interoperability standard on the basis of the VIMMP system of ontologies as well as MODA [20] was agreed between VIMMP and the Molecular Model
Database (MolMod DB) of the Boltzmann-Zuse Society [43]; the associated environment of interoperable platforms will prospectively also include Bottled SAFT [44].
The structure of the knowledge graph representing a molecular model is illustrated by Fig. 5.8, which corresponds to a two-centre Lennard-Jones plus pointquadrupole model (2CLJQ) where a molecule (in this case, acetylene) is represented
by a rigid unit (viso-am:rigid_object), consisting of two Lennard-Jones interaction
sites (viso-am:lj_site), a point-quadrupole site (viso-am:charge_quadrupole_site) as
well as a viso-am:structureless_object, representing the molecular centre of mass,
which is used the initial point of vov:relative_position vectors that indicate the coordinates of the interaction sites. The relation vov:has_attached_variable and subproperties of it are used to connect the interaction sites with the non-geometrical model
parameters, i.e. the mass associated with each of the two LJ sites (half the molecular
mass), the σ and site and energy parameters of the LJ potential, and a secondorder tensor characterizing the quadrupole moment. Other rigid molecular models
are described analogously.
The platform interoperability implementation developed on this basis employs
JSON-LD to exchange information on molecular models. Therefore, the knowledge
graph needs to be connected (i.e. it may not consist of multiple connected components), and its topology needs to be simplified to a tree structure such that each object
is subordinate to exactly one object, except for a single root node at the top. For the
present example, an osmo:workflow_graph with two sections, a use case (MODA