5.5 Documentation of Molecular Models
89
Sect. 5.1) and a model (MODA Sect. 5.2), is selected as the root of the tree. In this
way, e.g. one of the site coordinates is included in the rigid unit description as follows:
{
"@id": "acetylene:RIGID_UNIT",
"@type": "viso-am:rigid_object",
"vov:involves_object": [
{
"@id": "acetylene:COM",
"@type": "viso-am:structureless_object"
}, {
"@id": "acetylene:SITE_LJ_A",
"@type": ["viso-am:lj_site", "viso-am:mass_site"], ...
}, ...
],
"vov:involves_variable": [
{
"@id": "acetylene:LJ_A_POS",
"@type": ["osmo:logical_array", "vov:relative_position"],
"vov:has_initial_point": {"@id": "acetylene:COM"},
"vov:has_final_point": {"@id": "acetylene:SITE_LJ_A"}, ...
}, ...
]
}
The hierarchy by which objects are embedded in other objects in JSON is obtained
from a subset of the relations from the knowledge graph, shown in Fig. 5.8 as solid
arrows in blue colour, while references to IRIs are used to represent the other relations (dashed black arrows) in JSON-LD. The relations vov:involves_object and
vov:involves_variable are part of the JSON-LD tree structure (solid blue arrows),
so that COM, SITE_LJ_A, and LJ_A_POS are all hierarchically subordinate to
RIGID_UNIT. The relations vov:has_initial_point and vov:has_final_point, however,
are sideways connections between nodes from multiple branches of the tree (dashed
black arrows); therefore, their JSON-LD representation only points to the IRI of the
referenced object, using the "@id" keyword.
References
1. F. Abad Navarro, J.A. Bernabé Diaz, A. García Castro, J.T. Fernández Breis, Semantic publication of agricultural scientific literature using property graphs. Appl. Sci. 10(3), 861 (2020)
2. E. Katis, H. Kondylakis, G. Agathangelos, V. Kostas, Developing an ontology for curriculum
& syllabus, in Prof. ESWC, Satellite Events, ed. by A. Gangemi, A.L. Gentile, A.G. Nuzzolese,
M. Rudolph, S. Maleshkova, H. Paulheim, J.Z. Pan, M. Alam (Springer, Cham, Switzerland,
2018), pp. 55–59
3. G.J. Schmitz, Microstructure modeling in integrated computational materials engineering
(ICME) settings: can HDF5 provide the basis for an emerging standard for describing
microstructures? JOM 68(1), 77–83 (2016)
89
Sect. 5.1) and a model (MODA Sect. 5.2), is selected as the root of the tree. In this
way, e.g. one of the site coordinates is included in the rigid unit description as follows:
{
"@id": "acetylene:RIGID_UNIT",
"@type": "viso-am:rigid_object",
"vov:involves_object": [
{
"@id": "acetylene:COM",
"@type": "viso-am:structureless_object"
}, {
"@id": "acetylene:SITE_LJ_A",
"@type": ["viso-am:lj_site", "viso-am:mass_site"], ...
}, ...
],
"vov:involves_variable": [
{
"@id": "acetylene:LJ_A_POS",
"@type": ["osmo:logical_array", "vov:relative_position"],
"vov:has_initial_point": {"@id": "acetylene:COM"},
"vov:has_final_point": {"@id": "acetylene:SITE_LJ_A"}, ...
}, ...
]
}
The hierarchy by which objects are embedded in other objects in JSON is obtained
from a subset of the relations from the knowledge graph, shown in Fig. 5.8 as solid
arrows in blue colour, while references to IRIs are used to represent the other relations (dashed black arrows) in JSON-LD. The relations vov:involves_object and
vov:involves_variable are part of the JSON-LD tree structure (solid blue arrows),
so that COM, SITE_LJ_A, and LJ_A_POS are all hierarchically subordinate to
RIGID_UNIT. The relations vov:has_initial_point and vov:has_final_point, however,
are sideways connections between nodes from multiple branches of the tree (dashed
black arrows); therefore, their JSON-LD representation only points to the IRI of the
referenced object, using the "@id" keyword.
References
1. F. Abad Navarro, J.A. Bernabé Diaz, A. García Castro, J.T. Fernández Breis, Semantic publication of agricultural scientific literature using property graphs. Appl. Sci. 10(3), 861 (2020)
2. E. Katis, H. Kondylakis, G. Agathangelos, V. Kostas, Developing an ontology for curriculum
& syllabus, in Prof. ESWC, Satellite Events, ed. by A. Gangemi, A.L. Gentile, A.G. Nuzzolese,
M. Rudolph, S. Maleshkova, H. Paulheim, J.Z. Pan, M. Alam (Springer, Cham, Switzerland,
2018), pp. 55–59
3. G.J. Schmitz, Microstructure modeling in integrated computational materials engineering
(ICME) settings: can HDF5 provide the basis for an emerging standard for describing
microstructures? JOM 68(1), 77–83 (2016)