=Paper=
{{Paper
|id=Vol-1933/poster-paper-13
|storemode=property
|title=EcoPortal: A Proposition for a Semantic Repository Dedicated to Ecology and Biodiversity
|pdfUrl=https://ceur-ws.org/Vol-1933/poster-paper-13.pdf
|volume=Vol-1933
|authors=Nicola Fiore,Barbara Magagna,Doron Goldfarb
|dblpUrl=https://dblp.org/rec/conf/semweb/FioreMG17
}}
==EcoPortal: A Proposition for a Semantic Repository Dedicated to Ecology and Biodiversity==
https://ceur-ws.org/Vol-1933/poster-paper-13.pdf
EcoPortal: a proposition for a semantic repository
dedicated to ecology and biodiversity
Nicola Fiore1 [0000-0002-9538-2966], Barbara Magagna2 [0000-0003-2195-3997] and Doron Gold-
farb2 [0000-0003-1183-6041]
1
LifeWatch Italy, University of Salento, Lecce, Italy
2
Umweltbundesamt GmbH, Vienna, Austria
nicola.fiore@unisalento.it, barbara.magagna@umweltbundesamt.at,
doron.goldfarb@umweltbundesamt.at
Abstract. This paper presents the joint effort of LifeWatch Italy and LTER-
Europe to design EcoPortal, a semantic repository focused on ecology and bio-
diversity as well as on ecosystem observation mainly in the European context. It
is our aim to offer a space to collect domain ontologies as well as thesauri and
domain relevant reference lists. We plan to test NCBO BioPortal technology to
accommodate community requested functionalities.
Keywords: Registry · Ontology · Thesaurus ·Reference List · Semantics.
1 Introduction
To address today’s ecological challenges, it is necessary to use data coming from
different disciplines and providers. Thus, discovery and integration of data, especially
from the ecological domain, is highly labour-intensive and often ambiguous in seman-
tic terms. To improve the discovery, integration and re-usability of data the use of
semantic resources can help to harmonise and enrich the description of datasets and
its content. In the last decade research groups and infrastructures focusing in the mon-
itoring and analysis of ecosystem properties have increasingly put effort into the de-
velopment of semantic resources mainly based on core ontologies such as OBOE or
the O&M data model [1].
This paper presents the joint intention of the European networks LifeWatch Italy1
and LTER-Europe [2] to design a vocabulary repository focused on the ecology and
biodiversity research as well as on observation of biological and physical-
environmental data. This initiative will support the community in the management
and integration/alignment of their semantics and subsequently also of their data [3].
In order to increase interoperability between different domains and institutions,
LifeWatch Italy and LTER-Europe2 developed ontologies (LifeWatch Ontology3 and
1
http://www.lifewatchitaly.eu
2
http://www.lter-europe.net/
3
http://semantic.lifewatchitaly.eu
SERONTO4) as a semantic framework for integration of monitoring [4] and biodiver-
sity data and common vocabularies for harmonised data annotation (LifeWatch-Italy
Thesauri5, concerning functional traits, and EnvThes6 - Environmental Thesaurus [5]).
LifeWatch Italy and LTER-Europe are collaborating in order to improve and ex-
tend the existing thesauri and trace the semantic relations between them. In this con-
text, the lack of a common semantic repository for the ecological domain became
evident. We envisage to build a semantic platform for the domain to support not only
the joint work done by the infrastructures, but to be a robust and stable reference re-
pository for the European ecological community.
2 State of the art
Scientific communities are using an increasing number of ontologies or controlled
vocabularies to disambiguate the description of data. To make these vocabularies
discoverable and usable by software or by the community, different approaches exist:
Distributed RDF stores with SPARQL endpoints allowing to access vocabularies
using SPARQL queries. The presence of such endpoints does not solve the issue of
discoverability, as you must already be aware of the semantic resources by other
means to make use of them. To a certain extent they facilitate interoperability be-
tween different semantic resources but this requires high familiarity with the data
representation schema and the granularity of each federated source.
Semantic repositories (known also as ontology libraries [6]) are centralised access
points providing both discoverability and access to semantic resources.
The latter, on which this paper focuses on, are collections of ontologies and thesau-
ri with the primary purpose of enabling users to find and use them. They should be
distinguished from ontology search engines, such as Swoogle7, which automatically
crawl the Web to index ontologies rather than collect them. Also, we want to exclude
here collections on data, such as the Linked Open Data collection of datasets8.
According to the targeted user set approach of d’Aquin and Noy [6] different types
of repositories can be identified, although they often exist in a mixed form: curated
directories, registries and application platforms.
Many repositories already offer additional services, the most prominent ones are
BioPortal9 and EBI OLS10.
4
http://www.umweltbundesamt.at/fileadmin/site/daten/Ontologien/SERONTO/SERO
NTOCore20090205.owl
5
thesauri.lifewatchitaly.eu/
6
http://vocabs.ceh.ac.uk/evn/tbl/envthes.evn
7
http://swoogle.umbc.edu/2006/
8
https://www.w3.org/wiki/SweoIG/TaskForces/CommunityProjects/LinkingOpenData
9
http://bioportal.bioontology.org/
10
https://www.ebi.ac.uk/ols/index
We would also like to emphasise that most of the repositories are dedicated solely to
ontologies, some only contain thesauri like Finto11 and LusTRE12 and only a few
seem to offer the place to publish both ontologies and thesauri like AgroPortal13. The
inclusion of thesauri is important in our considerations because they are essential
sources of harmonised knowledge (not only) in the ecology domain.
3 EcoPortal
3.1 Requirement Elicitation: Purpose and Coverage
The main goal of the EcoPortal initiative is to provide a central registry for semantic
resources (e.g. vocabularies) used in the ecological and biodiversity domain allowing
users to identify and select semantic resources for specific tasks, as well as offering
generic services to exploit them in search, annotation or other scientific data man-
agement processes.
To reach this objective the user-centred, structured and systematic approach
AWARE (Analysis of WebApplication Requirements) has been adopted [7].
Following the AWARE guidelines, the following main stakeholders (i.e. user pro-
files to be considered for the Web application) have been identified:
─ Domain Expert, is the user of the portal and expert of the ecological domain. One
high-level goal of this kind of user is to explore the semantic world in the ecologi-
cal domain to understand how to annotate experimental data to enable interpreta-
tion, comparison, and discovery across databases. For this kind of user it is neces-
sary to offer very user-friendly tools and services.
─ Semantic Author, is a domain expert user that creates and shares a specific vocabu-
lary/ontology and is responsible to maintain it updated.
─ Semantic Engineer, is a type of user with semantic technology skills, who aims to
design new tools/services for the domain expert.
─ System Owner, who creates and manages EcoPortal and its services.
Figure 1 shows parts of the requirements analysis made for the stakeholder Domain
Expert. For each stakeholder we have identified goals and tasks (i.e. high-level user
activities on the site) and in the refined process they have been recompiled into re-
quirements. We can classify and synthesise the main requirements of the EcoPortal in
the following categories.
Content Requirements
The focus of the portal will be on the ecology, ecosystem and biodiversity do-
mains. Not only ontologies but also thesauri will be collected and managed.
Each semantic resource will be described by metadata (i.e. Structure Content
11
https://www.kansalliskirjasto.fi/en/services/system-platform-services/finto
12
http://linkeddata.ge.imati.cnr.it:2020/
13
http://agroportal.lirmm.fr/
Requirements in AWARE). The need of a common metadata set has been iden-
tified by several initiatives like OBO Foundry [8], LOV14 and AgroPortal.
Access Path and Navigation Requirements
─ Different search paths should be supported fitting the general requirements:
search within and across ontologies/thesauri, structured search via a SPARQL
query engine and advanced search will be developed. In the scenario in Figure 1
the Domain Expert needs to perform a search for “equivalent terms” and to nav-
igate from a term to the related one.
─ To facilitate the semantic resource discoverability, we want to use categories
(ecology, observation, etc.) as used in AgroPortal.
─ Browsing functionality will be offered including different types of visualisation
of the content. So, we aim to foresee automatic translations for single terms
wherever the vocabularies provide multilingual labels for them. Access services
will be also provided for all the resources, including ontologies/thesauri metada-
ta and the mappings between them.
─ We also intend to collect reference lists codified in SKOS used to define per-
missible values in certain data fields, providing information needed to make
other data meaningful and interpretable in an unambiguous way. Translating
from one reference list to another within the same domain is an essential need
for ecologists.
Fig. 1. Requirements for Domain Expert
System and User Operation Requirements
─ The portal should enable automatic (based on exact matching labels) as well as
manual mappings between semantic resources (private and/or public accessible -
14
http://lov.okfn.org/dataset/lov/
storing also metadata on mappings), and it should allow upload of mappings
created elsewhere.
─ For collecting resources, EcoPortal should use a hybrid approach: apart from the
administrators (ensuring to host the newest version of the resource also pub-
lished in other portals) also users should be enabled to submit their resources to
the collection through a dedicated user interface.
─ As far as belongs to gatekeeping, we envisage a two-step approach: after up-
loading, the semantic resource is validated by a quality committee, after that it is
published in the catalogue. But before validation the resource should already be
visible to the users labelled as not yet validated. Quality requirements should in-
clude metadata description, syntactically correctness and thematic relevance.
─ The portal should be able to automatically compute ontology metrics.
─ It should enable social interaction, allowing comments on ontologies and com-
ponents (at class level).
─ Instead of ranking ontologies by their relevance, we would prefer an exchange
information platform between supplier and user where it should become clear
for which use cases the resources were originally developed and then used. This
concept of semantic marketplace has been introduced at the EUDAT Semantic
Workshop15. We want to encourage developers to publish their vocabularies in
our Portal in an early stage of their development taking advantage of the domain
community.
3.2 Expected Contents.
A first inventory of the appropriate and relevant ontologies, thesauri and reference
lists to be hosted in the repository can be accessed online16. This list will be extended
by community contributions as collaborative and open process.
3.3 Conclusions and Future Work
The paper briefly introduces the ongoing work of LifeWatch Italy and LTER-Europe
in order to develop EcoPortal, a semantic repository focused on the ecosystem and
biodiversity research as well as on observation of the ecosystem. A common domain
specific repository of semantic resources allows their better integration into the work-
flows of metadata annotation (e.g. DEIMS-SDR17) and discovery. This fosters the
semantic interoperability not only on the metadata but also on the data level.
15
https://www.eudat.eu/events/trainings/co-located-eudat-semantic-working-group-workshop-
9th-rda-plenary-barcelona-3-4
16
http://www.servicecentrelifewatch.eu/web/ecoportal/wiki/-
/wiki/Main/EcoPortal+semantic+resources?_36_redirect=http%3A%2F%2Fwww.servicece
ntrelifewatch.eu%2Fweb%2Fecoportal%2Fwiki%2F-
%2Fwiki%2FMain%2Fall_pages%3Fp_r_p_185834411_title%3DEcoPortal%2Bsemantic%
2Bresources
17
https://data.lter-europe.net/deims/
A first prototype in line with the described architecture is planned to be online by
October 2017. In the initial phase, we will test the NCBO BioPortal technology to
accommodate community-requested functionalities with semantic resources of Euro-
pean networks. Considering the importance of such tools in the ecological field, we
expect a broad adoption of the EcoPortal in the community in the long run. Further-
more, LifeWatch as ERIC will be able to assure the long-term product sustainability.
The most pressing issues still to be addressed are the ability to manage and search
across different types of semantic resources like OWL ontologies and SKOS thesauri
as well as the use of a minimal metadata set and of a vocabulary marketplace consid-
ering the ongoing discussions in the RDA VSIG18.
4 Acknowledgments
The work is funded using resources from the ENVRIplus (H2020, Nr. 654182),
ECOPOTENTIAL (H2020, Nr. 641762) and eLTER (H2020, Nr. 654359) projects.
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18
https://www.rd-alliance.org/groups/vocabulary-services-interest-group.html