=Paper=
{{Paper
|id=None
|storemode=property
|title=Ontologies and Ontology Extension for Marine Environmental Information Systems
|pdfUrl=https://ceur-ws.org/Vol-679/paper11.pdf
|volume=Vol-679
|dblpUrl=https://dblp.org/rec/conf/enviroinfo/LeadbetterHLLD10
}}
==Ontologies and Ontology Extension for Marine Environmental Information Systems==
https://ceur-ws.org/Vol-679/paper11.pdf
Ontologies and Ontology Extension for Marine
Environmental Information Systems
Adam Leadbetter1 , Torill Hamre2 , Roy Lowry1 , Yassine Lassoued3 , and Declan
Dunne3
1
British Oceanographic Data Centre, Liverpool, United Kingdom
2
Nansen Environmental and Remote Sensing Center, Bergen, Norway
3
Coastal and Marine Resources Centre, Cork, Ireland
Abstract. An increasing number of data delivery and processing ser-
vices are available online from different environmental information sys-
tems. However, these services are often described using different termi-
nology and may therefore be difficult to find. Integrating services from
multiple providers and combining services into a workflow is likewise
complicated. Development of an interoperable environmental data portal
requires a detailed definition of the semantics of the data being requested
and the services being called. Existing descriptions of semantics, cap-
tured in controlled vocabularies or ontologies, represent valuable knowl-
edge that must be capitalised on. By ontology extension, we propose
to “bridge” existing semantic resources, with the potential to represent
more generic relationships and multilingual search and discovery. This
ontology extension will be part of a toolkit for building environmental
portals by means of standards for web-based data delivery and process-
ing services.
Key words: ontology extension, semantic infrastructure, marine envi-
ronmental information system, GMES, INSPIRE
1 Introduction
Today, a steadily growing wealth of marine data from a wide range of disciplines
acquired in real-time, near-real time and delayed mode, are available from online
information systems around the world. While substantial achievements have been
made in reaching consensus on standards for data and metadata formats, system
protocols and exchange mechanisms by standardisation organisations such as the
Open Geospatial Consortium, Inc. (OGC), the International Standardisation
Organization (ISO) and the World Wide Web Consortium (W3C), there are
still a number of gaps prohibiting full interoperability between environmental
information systems.
The NETMAR project [1] is part of the effort of the FP7 Information and
Communication Technologies (ICT) Programme to develop interoperable com-
ponents for the establishment of a Single Information Space in Europe for the En-
vironment (SISE) and Shared Environmental Information System (SEIS). NET-
MAR aims to build on the results of the FP6 projects ORCHESTRA and Seman-
tic Web services Interoperability for Geospatial Decision Making (SWING), plus
2 Ontologies and Ontology Extension for Marine Environmental Information Systems
the IST-FP7 integrated project Sensors Anywhere (SANY) to provide a toolkit
for building environmental portals in a coherent manner by means of chained
OGC Web Services (WxS), Open-source Project for a Network Data Access
Protocol (OPeNDAP) services and W3C standards controlled by Business Pro-
cess Execution Language (BPEL) workflow. NETMAR will also aim to utilise
results emerging from ongoing and new projects addressing interoperability in
environmental information systems.
The expected results of NETMAR will be a suite of components that can
be used by user communities interested in building a portal for marine environ-
mental data, and will offer search, download and integration tools for a range
of satellite, in situ and model data from open ocean and coastal areas. Further
processing of these data will also be available in order to provide statistics and
derived products suitable for decision making. Within NETMAR, this toolkit
will be used to develop a pilot European Marine Information System (EUMIS).
2 Ontologies for the Marine Domain
NETMAR has conducted a survey of existing ontologies that can be used as
building blocks for EUMIS and other Global Monitoring for Environment and
Security (GMES) downstream services and systems. Some of these are described
briefly below.
GEneral Multilingual Environmental Thesaurus (GEMET) [2] is a repository
maintained by the European Environment Information and Observation Network
(EIONET) using the procedural models specified in ISO 19135 ’Geographic in-
formation - Procedures for item registration’. GEMET has the potential to host
and serve multiple semantic resources (termed registers) maintained by sepa-
rate governance authorities under common technical governance. At the time
of writing, there are two registers: the GEMET concept thesaurus and the In-
frastructure for Spatial Information in Europe (INSPIRE) spatial data themes.
The GEMET concept thesaurus is a rich multilingual resource that should be
included in part if not in its entirety in the NETMAR semantic infrastructure.
The INSPIRE themes can be used to provide a semantic linkage to INSPIRE
for the NETMAR products and services.
The Natural Environment Research Council (NERC) Vocabulary Server (NVS)
[3] is a collection of controlled vocabularies that cover many subjects and facets
of the oceanographic domain. Currently, NVS holds some 135 publicly accessible
lists, of which 30 lists containing about 45% of all defined terms, were found to
be of interest to NETMAR. For instance, the SeaDataNet Parameter Disciplines
list that provides a hierarchy of topics/themes for parameter classification, sev-
eral other SeaDataNet vocabularies, as well as lists originating from the British
Oceanographic Data Centre, SeaVoX and several ISO standards. Many of the list
entries are linked together by a set of relationships that approximate to the Sim-
ple Knowledge Organisation System (SKOS) model. Therefore, the NVS could
become the base semantic resource on which the NETMAR extended ontology
is developed.
Ontologies and Ontology Extension for Marine Environmental Information Systems 3
The NASA Semantic Web for Earth and Environmental Terminology (SWEET)
ontologies [4] Version 2.0 (beta release as of August 2010) are a modular net-
work of 150 ontologies containing 4600 concepts. It was initially populated from
NASA’s Global Climate Change Master Directory (GCMD) Science Keywords,
but the content has undergone significant subsequent development. The network
is designed as a faceted upper-level ontology for Earth system science. Significant
emphasis has been placed on the development of orthogonal concepts that may
be combined to produce additional concepts. For example, the ontologies include
substances such as ’water’, ’air’ and ’blood’ and properties such as ’temperature’
rather than pre-combined concepts like ’air temperature’. This facilitates discov-
ery searches along either the substance axis or the property axis.
Other identified semantic resources include the GCMD; Marine Metadata
interoperability’s (MMI) Ontology Repository & Registery (ORR); the Interna-
tional Council for the Exploration of the Seas (ICES) Reference Code (RECO)
system; the United States Geological Survey (USGS) Thesaurus; the USGS In-
formation Bank; data and keyword ontologies from the InterRisk project; Geo-
science Markup Language (GeoSciML) vocabularies; World Register of Marine
Species (WoRMS) Aphia Records; and Quantities, Units, Dimensions and Types
(QUDT) ontologies.
3 Ontology Extension
To develop an interoperable environmental data portal, the NETMAR project
requires a detailed definition of the semantics of the data being requested and
the services being called. A major goal of the project is therefore to develop a
multi-domain and multilingual ontology of marine data and services to provide
semantic interoperability [5] within the system. This will allow searching across
human languages as well as across scientific domains. In order to achieve this,
NETMAR will focus on data sets described by metadata records which adhere
to the ISO19115 standard in which the fields are populated from controlled vo-
cabularies. Initially, NETMAR will also only support data marked up in English,
but these data will be discoverable in a variety of human languages.
The approach taken to building an ontology for NETMAR will be to analyse
existing semantic resources and provide mappings between them, gluing together
the definitions and worksflows of the OGC WxS services. The concept of ontol-
ogy extension is well documented in such domains as computer science [6, 7],
bioinformatics [8] and eLearning [9], but has not previously been demonstrated
in the oceanographic community. The mappings between the terms aim to be
more general than the standard “narrower than”, “broader than” type seen in
the thesauri or simple ontologies implemented by previous projects. Tools for the
development and population of ontologies will also be needed in the semantic
infrastructure. NETMAR will provide such tools for selected parts of the marine
domain as there will be instances in which existing resources cannot sufficiently
describe newly encountered data or services.
4 Ontologies and Ontology Extension for Marine Environmental Information Systems
Fig. 1 shows a flow chart for the process of ontology extension in NETMAR.
An existing ontology typically represents knowledge within a single domain, with
“simple” or “richer” relationships between the concepts. Besides describing the
domains, an ontology gives the ability to reason about the concepts and their
relationships. If the ontology on the other hand is extended, i.e. linked to other
ontologies, it is possible to increase the breadth and depth of the represented
knowledge and also infer knowledge across domains. Linking to multilingual on-
tologies further extends the reasoning capabilities by allowing the user to specify
search parameter in their native language, while the semantic infrastructure will
also find resources described using these same or related terms in other human
languages. Ontology extensions and the use of multilingual ontologies further
enable the chaining of web and data processing services, by allowing verification
that the input data to each processing step fulfil given criteria.
Fig. 1. A flow chart for the process of ontology extension within NETMAR (after [10]).
There are a number of challenges presented by ontology extension, and the
literature contains a range of automated and semi-automated schemes to over-
come these issues [11]. However, due to the domain specificity of the NETMAR
Ontologies and Ontology Extension for Marine Environmental Information Systems 5
project, a manual approach is to be used. The major imitations of this approach
are that the ontologies being extended have been developed without being made
interoperable and that human identification of related semantic concepts is re-
quired in order to produce the mappings between the various semantic resources.
This is a time consuming process, and one which requires science domain exper-
tise but is possibly open to human error, and as such the construction of the
NETMAR extended ontology will take time and effort. The formation of a NET-
MAR ontology governance body [12] goes some way to mitigating the concerns
over domain knowledge and human error.
It would be possible to use programmatic methods to produce the extended
ontology, but as noted in [13] the re-use of existing algorithms for this purpose is
difficult, in part due to the heterogeneous nature of the distributed resources [8],
and the need for human validation is not removed. The identified base semantic
resource for NETMAR [1] contains some 100,000+ mappings which have been
generated by hand and these mappings already bridge between several of the
semantic resources identified above. As such the NETMAR ontology will be able
to operationally support “smart” discovery (a search for “precipitation” returns
concepts also labelled “rain”, “pluie”, “Regen” etc. [14]) of concepts, products
and services, which has previously only been demonstrated using small, custom
built ontologies.
4 Semantic Infrastructure
Standard technologies and tools are needed to develop a semantic infrastruc-
ture that supports the planned ontology extensions and tools for creation and
management of semantic resources, web service and processing workflows. NET-
MAR has conducted a survey of ontology and semantic framework technologies.
Due to the broad compatibility between its members, its recommendation by
the W3C and its large software base, we recommend the use of the Resource
Description Framework (RDF) family of languages to represent ontologies. The
SPARQL Protocol and RDF Query Language (SPARQL) is the recommended
query language due to the ubiquitous nature of support for it and its high level of
extensibility. For ontology publication, the Mulgara server has the easiest mech-
anisms for entering data and then querying it, with a simple HyperText Transfer
Protocol (HTTP) interface to a SPARQL and interactive Tucana Query Lan-
guage (iTQL) endpoint.
Jena is a powerful complete ontology framework that provides two mech-
anisms for storing data, one as a wrapper to a relational database, the other
using a bespoke system similar to the Mulgara server. The querying mecha-
nism is an extension of SPARQL called ARQ which provides access to Extensi-
ble Stylesheet Language Transformations (XSLT) functions that make complex
queries possible. Jena also provides classes for creating and editing ontologies
programmatically.
Additional tools needed include an ontology editor and a concept mapping
tool, for which Semantic Turkey and CMAPTools Ontology Editor are recom-
6 Ontologies and Ontology Extension for Marine Environmental Information Systems
mended within the NETMAR project. Other tools, such as Protégé SWOOP and
PoolParty were reviewed [15] but found to be lacking for the needs of the NET-
MAR project, on the whole due to problems loading large (20,000+ terms) vocab-
ularies into these tools. The Marine Metadata Interoperability (MMI) project’s
Vocabulary Integration Environment may be utilised to build bridges between
ontologies stored in the MMI Ontology Registry and Repository and other se-
mantic resources.
Several semantic frameworks have been developed over the past few years
for Earth Information Systems (EIS). A review of the most popular ones has
been carried out as part of NETMAR [16]. The review included, but was not
limited to, the InterRisk semantic framework [17], the International Coastal At-
las Network prototype mediator [18], the MMI and the Ocean Observatories
Initiative (OOI) semantic frameworks [19], the ORCHESTRA Semantic Cata-
logue Architecture [20], and OOSTethys [21]. These existing semantic frame-
works have been designed for various purposes (data/metadata interoperability,
data discovery, etc.) and therefore offer different capabilities and functionalities.
Nevertheless, they all deal with simple resources such as datasets, documents
or non-complex data and metadata services with limited types of relationships
(in general: broader term; narrower term; equivalent term; and related term).
The semantic infrastructure provided by NETMAR will aim to move beyond
the approach of existing frameworks. Using the tools described above, the ex-
tended ontology and a richer set of relationships, the semantic infrastructure will
support functional interoperability [5] through the discovery of complex services
(such as OGC Web Processing Services), allow service chaining and describe the
propagation of uncertainty through the processing scheme.
5 Conclusions
Development of an interoperable environmental data portal requires a detailed
definition of the semantics of the data being requested and the services being
called. NETMAR has therefore identified a number of ontologies, both specific to
the marine domain as well as more generic resources that can be used as building
blocks in a semantic infrastructure. These semantic resources will be analysed
and mappings provided between them, to extend the different resources, thus al-
lowing cross-resource search and discovery. In addition, the ontology extensions
will form the basis for the semantic infrastructure that will support chaining
of OGC WxS services, where for each step it can be verified that the proposed
input data satisfy the criteria for the service. By integrating the semantic in-
frastructure into the data and processing elements it will be possible to enforce
correct connections between components (e.g. do not send chlorophyll data to
a component that only knows how to process sea surface temperature data). It
also becomes possible to pass additional metadata along the chain, such as the
error introduced by each component.
The NETMAR project approach makes possible the reuse and building upon
the large number of concepts and relationships already defined by existing se-
Ontologies and Ontology Extension for Marine Environmental Information Systems 7
mantic resources, while facilitating more generic relationships in extensions. It
is expected that the methodology for the ontology extensions will be applicable
to other domains.
Acknowledgement
The NETMAR (Open service network for marine environmental data) project
is supported by the European Union Framework Programme 7, under grant
agreement no. 249024.
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