58
4 Semantic Technology for Simulations and Molecular Particle-Based Methods
In a nutshell, UML allows to describe a system
2 structure and behaviour via
different types of diagrams. It was motivated as a unifying object-oriented language,
and one of its main aims is to “advance the state of the industry by enabling object
visual modeling tool interoperability” [29]. The visual aspect of the diagrams can be
used to share ideas; however, these diagrams can also be given “life”, in the sense of
visual programming.
The OMG standards are widely adopted and there are many (commercial and not)
tools based on UML that allow, for example, to generate executable code, check the
model and generate test suites.
Of course, “modeling” in the case of UML has a more general meaning (as abstraction) than as we intend it in the EMMC sense (as applied to materials and based on
physics and mathematics). From the literature, we note that UML does not appear to
be strongly connected to science applications, but it is probably used internally by
professional software tools, including those commonly used in engineering.
Finally, an important contribution bridging between UML and ontologies is
OntoUML, which is ontologically well-founded version of UML (more specifically,
of the UML 2.0 fragment of class diagrams) [16, 17].
4.3 Software Capabilities
The aim of the VImmp Ontology of Software (VISO)
3 is to characterize software tools
in the area of materials modelling, especially their features (i.e. capabilities), intended
both at the model and solver level, but also their technical requirements, compatibility
with other tools and licensing aspects. The concepts defined within this ontology will,
first, guide the ingest of information on the VIMMP platform, and, later, allow the
users to retrieve and compare tools. Below an upper level (viso-general, cf. Fig. 4.1)
that addresses aspects common to all software, we split VISO into three branches
focusing on classes of models: electronic (EL, viso-el), atomistic and mesoscopic
(AM, viso-am), and continuum (CO, viso-co) models.
4 These branches depend on
viso-general, but can be loaded independently of the other two siblings. We underline
that both VISO and VOV (presented in the next section) are designed to address
models from the four granularity levels of RoMM [30]. However, in this book, we
2 A “system” is intended here in a very general sense, as something made of components.
3 VISO: https://purl.vimmp.eu/semantics/viso/viso-general.ttl, https:
//purl.vimmp.eu/semantics/viso/viso-electronic.ttl, https://purl.
vimmp.eu/semantics/viso/viso-atomistic-mesoscopic.ttl,
https://
purl.vimmp.eu/semantics/viso/viso-continuum.ttl
(all
of
which
are non-resolvable IRI); the concatenation of the four files is mirrored at
http://www.molmod.info/semantics/viso-all-branches.ttl
(resolvable
URL).
4 To avoid name clashes between the branches, prefixes are used as indicated. In the protégé editor,
one can choose different options for the rendering (view tab), including rendering by short name
and rendering by prefixed name.
4 Semantic Technology for Simulations and Molecular Particle-Based Methods
In a nutshell, UML allows to describe a system
2 structure and behaviour via
different types of diagrams. It was motivated as a unifying object-oriented language,
and one of its main aims is to “advance the state of the industry by enabling object
visual modeling tool interoperability” [29]. The visual aspect of the diagrams can be
used to share ideas; however, these diagrams can also be given “life”, in the sense of
visual programming.
The OMG standards are widely adopted and there are many (commercial and not)
tools based on UML that allow, for example, to generate executable code, check the
model and generate test suites.
Of course, “modeling” in the case of UML has a more general meaning (as abstraction) than as we intend it in the EMMC sense (as applied to materials and based on
physics and mathematics). From the literature, we note that UML does not appear to
be strongly connected to science applications, but it is probably used internally by
professional software tools, including those commonly used in engineering.
Finally, an important contribution bridging between UML and ontologies is
OntoUML, which is ontologically well-founded version of UML (more specifically,
of the UML 2.0 fragment of class diagrams) [16, 17].
4.3 Software Capabilities
The aim of the VImmp Ontology of Software (VISO)
3 is to characterize software tools
in the area of materials modelling, especially their features (i.e. capabilities), intended
both at the model and solver level, but also their technical requirements, compatibility
with other tools and licensing aspects. The concepts defined within this ontology will,
first, guide the ingest of information on the VIMMP platform, and, later, allow the
users to retrieve and compare tools. Below an upper level (viso-general, cf. Fig. 4.1)
that addresses aspects common to all software, we split VISO into three branches
focusing on classes of models: electronic (EL, viso-el), atomistic and mesoscopic
(AM, viso-am), and continuum (CO, viso-co) models.
4 These branches depend on
viso-general, but can be loaded independently of the other two siblings. We underline
that both VISO and VOV (presented in the next section) are designed to address
models from the four granularity levels of RoMM [30]. However, in this book, we
2 A “system” is intended here in a very general sense, as something made of components.
3 VISO: https://purl.vimmp.eu/semantics/viso/viso-general.ttl, https:
//purl.vimmp.eu/semantics/viso/viso-electronic.ttl, https://purl.
vimmp.eu/semantics/viso/viso-atomistic-mesoscopic.ttl,
https://
purl.vimmp.eu/semantics/viso/viso-continuum.ttl
(all
of
which
are non-resolvable IRI); the concatenation of the four files is mirrored at
http://www.molmod.info/semantics/viso-all-branches.ttl
(resolvable
URL).
4 To avoid name clashes between the branches, prefixes are used as indicated. In the protégé editor,
one can choose different options for the rendering (view tab), including rendering by short name
and rendering by prefixed name.