# The EarthPortal, towards an ontology repository for the Earth System semantic artefacts

Christelle Pierkot, Guillaume Alviset, Marine Vernet

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Christelle Pierkot, Guillaume Alviset, Marine Vernet. The EarthPortal, towards an ontology repository for the Earth System semantic artefacts. Onto4FAIR, Sep 2023, Leipzig, Germany. hal-04908666

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# The EarthPortal, towards an ontology repository for the Earth System semantic artefacts

Guillaume ALVISET<sup>a</sup>, Christelle PIERKOT<sup>a</sup> and Marine VERNET<sup>a</sup>

<sup>a</sup>IR Data Terra-CNRS

ORCID ID: Guillaume Alviset https://orcid.org/0009-0004-4295-6593, Christelle

Pierkot https://orcid.org/0000-0002-2591-3311, Marine Vernet

https://orcid.org/0000-0002-39906-5579

**Abstract.** In order to describe research data in a standard and FAIR way, Earth and Environmental research communities have developed and manage heterogeneously separate vocabularies, thesauri and ontologies which, when conducting interdisciplinary studies, lead to discovery, interoperability and semantic search challenges. To address this, this article proposes the use of an ontology repository to store, expose, catalog and map semantic artefacts. The chosen approach is based on the mature and flexible OntoPortal technology to create the EarthPortal, a dedicated prototype for Earth and environmental sciences within the framework of the FAIR-IMPACT project and in strong collaboration with user-communities. It will therefore make sure to include all functionalities required to address issues mentioned above to ensure semantic artefacts quality.

**Keywords.** Ontology repository, Earth sciences, Ontoportal, FAIR, semantic artefacts catalogue

## 1. Introduction

As in other scientific fields, the communities involved in the Earth system need access to semantic artefacts [1] for different purposes (data integration, metadata management, semantic search, etc.). However, vocabularies have been developed independently for each of the different compartments of the Earth System (atmosphere, land surfaces, solid earth and sea), and have not been defined in a transdisciplinary way. Today, these domains have to work together to conduct their scientific research, and they need to evolve their practices and find better ways of combining and matching the different semantic artefacts in an effective manner and in a FAIR way[2]. To achieve this, one approach is to use an ontology repository to store and catalogue the various semantic artefacts (from vocabularies to ontologies) for Earth systems. It provides a centralized catalogue which allows to create and store mappings between concepts from different domains. Assessing the FAIRness of the stored semantic artefacts also becomes easier. The FAIR-IMPACT project supports the implementation of FAIR-enabling practices, tools and services across scientific communities at a European, national and institutional level. The work-package 4 “Metadata and Ontologies” deals with greater
and more harmonised use of semantic artefacts, leading to semantic interoperability between disciplines. In this perspective, implementation of semantic artefacts catalogues by new communities is supported. The approach described in this paper fits into this context.

After reviewing the different practices and tools [3] used by our communities to share and expose their semantic artefacts, we will focus on the solution chosen, the reasons for choosing this solution and the improvements planned to ensure that this ontology repository meets the requirements of the Earth System and Environmental Communities.

## 2. Semantic Artefact Management in Earth and Environmental Sciences

The two semantic artefacts commonly used in the Earth and Environmental Sciences are the SWEET ontology<fnref n="1" /> (Semantic Web for Earth and Environment Technology Ontology) defined by the Semantic Technologies Group of ESIP<fnref n="2" />, and the GCMD Thesaurus (Global Change Master Directory) defined by the NASA Earth Science Data Systems<fnref n="3" />. However, since these semantic artefacts are high-level and do not cover all the features of the Earth System, some initiatives have been done by the communities to define dedicated semantic artefacts. In France, the Data Terra Research Infrastructure which covers the four Earth System compartments, has specified the vocabularies for each of them (Theia/Ozcar<fnref n="4" />, Aeris<fnref n="5" />, Odatis<fnref n="6" /> and Formater<fnref n="7" />), and is in the process of developing an ontology, based on the SOSA ontology [4], including different type of concepts (variables, platforms, sensors, feature types).

The climate community has also defined the Climate Analysis (CA) ontology [5] based on the SOSA ontology with the addition of meteorological and geographic elements associated terms. At the European level, Actris<fnref n="8" />, the research infrastructure supporting research into climate and air quality has built a controlled vocabulary<fnref n="9" />. EPOS, the infrastructure for the solid earth compartment is in the process of specifying its own<fnref n="10" />. The NERC Vocabulary server gives access to standardised and hierarchically organized vocabularies, for the oceanographic and associated domains [6]. For the environmental domain, the ENVO<fnref n="11" /> ontology which represents knowledge about environments, environmental processes, ecosystems, habitats, and related entities has been set-up.

All these semantic artefacts, from vocabularies and thesauri to ontologies, need to be managed into specialized repositories in order to be used and shared by communities:

<footnote n="1">¹https://github.com/ESIPFed/sweet</footnote>

<footnote n="2">²https://wiki.esipfed.org/Semantic_Technologies</footnote>

<footnote n="3">³https://www.earthdata.nasa.gov/esds</footnote>

<footnote n="4">⁴https://in-situ.theia-land.fr\skosmos\theia_ozcar_thesaurus/en/</footnote>

<footnote n="5">⁵https://skosmos.aeris-data.fr/</footnote>

<footnote n="6">⁶https://vocab.ifremer.fr/</footnote>

<footnote n="7">⁷https://catalogue-terresolide.ipgp.fr/voc/discipline/en/</footnote>

<footnote n="8">⁸https://www.actris.eu/</footnote>

<footnote n="9">⁹https://vocabulary.actris Nilu.no/skosmos/actris_vocab/en/index</footnote>

<footnote n="10">¹⁰https://registry.epos-eu.org/ncl</footnote>

<footnote n="11">¹¹https://www.ebi.ac.uk/ols/ontologies/envo</footnote>
* OLS [7] provided by the EliXir community is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions. OLS has been chosen by the ENVO ontology to share the concept for the Environmental domain. However, the current version of OLS (OLS3) is no longer updated but it will be replaced by a newer on the end of October 2023. Unfortunately, it is not capable of hosting something else than ontologies in OBO and OWL formats.

* Skosmos [8] is an open source web-based SKOS browser and publishing tool, mainly used to access controlled vocabularies for indexing, information retrieval and vocabulary development. Skosmos has been adopted by some communities to specify their vocabularies, such as the atmospheric one (e.g. AERIS and ACTRIS research infrastructures have both used Skosmos). Nevertheless, it is strictly restricted to the usage of SKOS and do not support ontologies.

* VocPrez is a tool (API and web front-end) for the read-only delivery system of SKOS vocabularies, compliant with Content Negotiation by Profile. It has been adopted by the NERC Vocabulary Server from the BODC [9], the OGC Definition server or the British Geological Survey. However, VocPrez is restricted to a custom implementation of SKOS which can require adjustments if used with other tools. Its read-only structure also not suitable for users to be able to submit their own semantic artefacts.

* UKGovLD is a Linked Data Registry developed by the UK Government, to manage code lists or controlled vocabularies, which support content negotiation. It provides a service to create and manage controlled, authoritative lists of identifiers as URIs. It is used by the French geological survey (BRGM) to define and expose their vocabularies and by the French Data Terra RI, as a FAIR incubator for the concepts used by its data clusters. Similarly to other vocabulary browsers, it does not support ontologies.

* LOV (Linked Open Vocabularies) is a catalogue of reusable vocabularies for the description of data on the Web. LOV supports Vocabulary Search, Vocabulary Assessment, Vocabulary Mapping [10]. Anyway, it does not provide any service beyond cataloguing vocabularies.

* Ontoportal is an open source and generic technology to build ontology repositories or semantic artefact catalogues which has been set-up by Stanford University in 2005, for the biomedical ontologies with the BioPortal appliance [11]. The technology was first reused by the Agrifood communities with the release of AgroPortal [12]. More communities adopted then this technology, with the addition of EcoPortal for the ecology part [13], MatPortal for materials science, IndustryPortal for industry and related domains.

### 3. Ontoportal and Ontoportal Alliance

The overview of the panel of technologies that we have seen previously makes one of the solutions stand out of the others: Ontoportal. This open source ontology repository and semantic artefact catalogue has several advantages over the others[3]:

* It regroups the features of some other technologies and combine them with new ones, such as mappings creations and storage, FAIRness assessment, text
annotation, version management, a REST API to read and write content. It has
the advantage of being domain agnostic and support a wide range of semantic
artefacts from SKOS thesauri to complex ontologies in different formats.

* It is actively maintained, the Ontoportal alliance is regularly pushing fixes and new features through the centralization of the code repository

* The technology is well proven today. OntoPortal comes from the NCBO BioPortal that is available since 2005 and is widely used across biomedical communities but also with AgroPortal and the agrifood community.

* It can be easily deployed in a pre-configured Open Virtual Machine Format (OVF) appliance<fnref n="12" />.

The OntoPortal initiative comes back from 2005, where the BioPortal code is first re-used for agrifood communities leading to the release of AgroPortal. More communities adopted then this technology, with the addition of EcoPortal, MedPortal, SIFR Bioportal, IndustryPortal and MatPortal, publicly available. All of these are part of the consortium known as the OntoPortal Alliance. The source code is located in a common repository which is then forked by each alliance member, making all public OntoPortal instances connected to it. This makes the feature development and integration easier: a community can merge code back to the shared repository, which can be then pulled to other communities in a streamlined workflow.

The choice of OntoPortal answers most of the issues currently encountered in
the Earth systems community concerning semantic artefacts. There is a strong need
of unifying multidisciplinary workflows to ensure semantic artefacts are up to FAIR
standards, which can be answered with the tools available in OntoPortal. Moreover, the
deployment of additional instances of OntoPortal for different thematics opens some
opportunities, such as an inter-portal federation. While each domain has their own set of
resources, there are still some of them that can be found overlapping with others (as in
Earth sciences can overlap with Ecology, so EarthPortal with EcoPortal). While this is
still at the stage of an idea, portals federation could enrich existing resources with even
more links to related material to push multidisciplinary workflows and avoid duplication.

4. The EarthPortal

Earth sciences being multidisciplinary by nature, each sub-domain follows its own
conventions in the creation and usage of semantic artefacts. However, when it comes to
working together, it is common to witness similarities between standards, which then
require to be manually curated to provide the necessary data and metadata crosswalks
for joint efforts. For example, volcanologists and atmospheric specialists have to rely on
space-based observations to track the evolution of eruptive activity in near real-time. To
achieve this, scientists need to find and aggregate relevant datasets from Solid Earth and
Atmospheric communities. This can be done by using an Interdisciplinary Discovery and
Access Service [14] which can provide users with an easy and FAIR service for discovery
and access to multidisciplinary and aggregated data sets. This service has to rely on
a semantic component to ensure that the discovery process is as efficient as possible.
The EarthPortal, the Ontoportal instance that will be dedicated to Earth systems, will

<footnote n="12">¹²https://ontoportal.github.io/documentation/administration/steps/getting_started</footnote>
centralize and catalog semantic artefacts from all sub-domains, to meet the following needs:

* Better discovery of the semantic artefacts used in Earth sciences. They are currently scattered across a significant amount of repositories even at sub-domain level, if available on the web at all.

* Providing the necessary tools for interdisciplinary work. This will be mainly done by storing and creating mappings between vocabularies and ontologies from different sub-domains.

* Assess the FAIRness of semantic artefacts. While their usage is strongly recomm- -ended for data and metadata to be FAIR, vocabularies and ontologies also need their own metadata to reach FAIR standards. Although depositing artefacts in the repository already gives a certain level of FAIRness, the user must provide additional informations about their submissions. The O'FAIRE [15] tool initially developed by the AgroPortal team will be used in that regard.

The EarthPortal will allow users to submit their own semantic artefacts, but will also contain links to existing vocabularies and ontologies. Since it is not possible to ask all actors from Earth science communities (or even broader communities in the case of multidisciplinary standards) to store all their resources into the same repository, the OntoPortal technology also allows external resources to be referenced and work with as if they were included. This initiative being driven at a general level, the usage of EarthPortal can see the emergence of requests from the different Earth systems communities, leading to the development of new features. One of the leads towards the evolution of this technology concerns semantic artefacts mapping. Similarly to data and semantic artefacts, mappings can also embed metadata. While most of the information is similar, mappings are also subject to automation (i.e. lexical matching) which then deliver additional metadata about the results of this automation process. SSSOM [16] might be a good candidate to issue standards concerning mapping sharing. Since it is one of the main features of the EarthPortal, integration of SSSOM is being considered.

5. Conclusions

The usage of the OntoPortal technology to manage Earth system semantic artefacts is motivated by the panel of tools and flexibility it provides. Its dedicated instance for Earth science called EarthPortal will be part of the OntoPortal alliance, which brings potential for collaborations with other members. Not only it offers additional technical insight but also a way to support the EarthPortal in its early stages, to manage user feedback and develop new features. The first step will be to collect and reference the semantic artefacts used in each sub-domain of Earth system, then enrich them with mappings and metadata to ensure compliance with the FAIR principles. Of course, this is not without a cost. Users might not understand the entire scope of the thesauri, vocabularies and ontologies they use nor do they have the knowledge to do so. The EarthPortal will bring all the necessary features to lower the entry bar for the creation and usage of semantic artefacts by listening to feedback from each community and developing the corresponding features. Furthermore, in the context of a collaboration between FAIR IMPACT, in charge of the EarthPortal development, and FAIR-EASE, another European
project, the content of the EarthPortal repository could be used to enhance the semantic
analyser planned by the FAIR-EASE project.

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