5.1 Representing Scenarios
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corresponding semantic annotation [3], e.g. the H5MD format [4] for semantically
enriched data in molecular modelling and simulation. The VIMMP marketplace
platform API and its Zontal Space back end permit handling annotated digital objects
through the HDF5-based Allotrope Data Format (ADF) [5–7].
5.2 Top-Level Ontology
For a fundamental philosophical underpinning, the European Materials and Modelling Ontology [8, 9] relies on a combination of physicalist mereotopology following Varzi [10] and a nominalist reinterpretation of Peirce’s semiotics [11]. Therein,
physicalist mereotopology primarily addresses the description of materials, which
is extended by nominalist semiotics to describe modelling, simulation and experiments. For a discussion of nominalism, cf. Lewis [12], more specific implications of
the approach of the EMMO on representing modelling and simulation of physical
systems have been discussed elsewhere [13].
To facilitate the top-level ontology alignment of the VIMMP ontologies, a module
with a scaled-down EMMO in TTL format is included, EMMO version 1 simplified
(EMMO1s), which at the present stage (version 1.0.4) is based on EMMO version 1.0.0 alpha 2 (April 2020). EMMO1s provides user-friendly IRIs for EMMO
concepts,
2 retaining the labels, e.g. the IRI of the EMMO concept with rdfs:label
“Semiosis” is given in the original EMMO as emmo-semiotics:EMMO_008fd3b2_
4013_451f_8827_52bceab11841. For these entities, EMMO1s specifies aliases that
can be accessed directly through the label, such as emmo1s:Semiosis. In the interest
of notational clarity, to indicate the origin of the concept definitions and the respective
EMMO modules, these entities will here be denoted by the EMMO prefix followed
by the EMMO1s suffix, e.g. by emmo-semiotics:Semiosis, even though internally,
for VIMMP, it is actually emmo1s:Semiosis.
The VIMMP Primitives (VIPRS) module amplifies the ways in which the EMMObased top-level semantic interoperability architecture can be applied to the relations
characterizing metadata from the VIMMP marketplace-level domain ontologies.
3
With this aim, VIPRS extends the EMMO system of top-level relations by three
features:
1. modal logic (e.g. Kripke semantics) and modal squares of opposition;
2. concatenation of mereotopological and semiotic relations, yielding mereosemiotic
relations;
3. top-level datatype properties.
2 EMMO1s: https://purl.vimmp.eu/semantics/alignment/emmo1s.ttl (nonresolvable IRI), mirrored at http://www.molmod.info/semantics/emmo1s.ttl
(resolvable URL).
3 VIPRS: https://purl.vimmp.eu/semantics/alignment/viprs.ttl (nonresolvable IRI), mirrored at http://www.molmod.info/semantics/viprs.ttl
(resolvable URL).
75
corresponding semantic annotation [3], e.g. the H5MD format [4] for semantically
enriched data in molecular modelling and simulation. The VIMMP marketplace
platform API and its Zontal Space back end permit handling annotated digital objects
through the HDF5-based Allotrope Data Format (ADF) [5–7].
5.2 Top-Level Ontology
For a fundamental philosophical underpinning, the European Materials and Modelling Ontology [8, 9] relies on a combination of physicalist mereotopology following Varzi [10] and a nominalist reinterpretation of Peirce’s semiotics [11]. Therein,
physicalist mereotopology primarily addresses the description of materials, which
is extended by nominalist semiotics to describe modelling, simulation and experiments. For a discussion of nominalism, cf. Lewis [12], more specific implications of
the approach of the EMMO on representing modelling and simulation of physical
systems have been discussed elsewhere [13].
To facilitate the top-level ontology alignment of the VIMMP ontologies, a module
with a scaled-down EMMO in TTL format is included, EMMO version 1 simplified
(EMMO1s), which at the present stage (version 1.0.4) is based on EMMO version 1.0.0 alpha 2 (April 2020). EMMO1s provides user-friendly IRIs for EMMO
concepts,
2 retaining the labels, e.g. the IRI of the EMMO concept with rdfs:label
“Semiosis” is given in the original EMMO as emmo-semiotics:EMMO_008fd3b2_
4013_451f_8827_52bceab11841. For these entities, EMMO1s specifies aliases that
can be accessed directly through the label, such as emmo1s:Semiosis. In the interest
of notational clarity, to indicate the origin of the concept definitions and the respective
EMMO modules, these entities will here be denoted by the EMMO prefix followed
by the EMMO1s suffix, e.g. by emmo-semiotics:Semiosis, even though internally,
for VIMMP, it is actually emmo1s:Semiosis.
The VIMMP Primitives (VIPRS) module amplifies the ways in which the EMMObased top-level semantic interoperability architecture can be applied to the relations
characterizing metadata from the VIMMP marketplace-level domain ontologies.
3
With this aim, VIPRS extends the EMMO system of top-level relations by three
features:
1. modal logic (e.g. Kripke semantics) and modal squares of opposition;
2. concatenation of mereotopological and semiotic relations, yielding mereosemiotic
relations;
3. top-level datatype properties.
2 EMMO1s: https://purl.vimmp.eu/semantics/alignment/emmo1s.ttl (nonresolvable IRI), mirrored at http://www.molmod.info/semantics/emmo1s.ttl
(resolvable URL).
3 VIPRS: https://purl.vimmp.eu/semantics/alignment/viprs.ttl (nonresolvable IRI), mirrored at http://www.molmod.info/semantics/viprs.ttl
(resolvable URL).