=Paper=
{{Paper
|id=Vol-2969/paper6-s4biodiv
|storemode=property
|title=EcoPortal: An Environment for FAIR Semantic Resources in the Ecological Domain
|pdfUrl=https://ceur-ws.org/Vol-2969/paper6-s4biodiv.pdf
|volume=Vol-2969
|authors=Xeni Kechagioglou,Lucia Vaira,Pierfrancesco Tomassino,Nicola Fiore,Alberto Basset,Ilaria Rosati
|dblpUrl=https://dblp.org/rec/conf/jowo/KechagioglouVTF21
}}
==EcoPortal: An Environment for FAIR Semantic Resources in the Ecological Domain==
https://ceur-ws.org/Vol-2969/paper6-s4biodiv.pdf
EcoPortal: An Environment for FAIR Semantic Resources in the
Ecological Domain
Xeni Kechagioglou 1, Lucia Vaira 1, Pierfrancesco Tomassino 2, Nicola Fiore 1, Alberto Basset
1,2,3
and Ilaria Rosati 2
1
LifeWatch ERIC, Service Centre, S.P. Lecce-Monteroni – Ecotekne, Lecce, 73100, Italy
2
Institute of Research on Terrestrial Ecosystems (IRET), National Research Council (CNR), Via Salaria Km
29.300, 00015 Monterotondo Stazione, Rome, Italy
3
University of Salento, Department of Biological and Environmental Sciences and Technologies, S.P. Lecce-
Monteroni – Ecotekne, Lecce, 73100, Italy
Abstract
Ecological semantic resources are being increasingly required by researchers. To improve their
FAIRness, LifeWatch ERIC launched a repository to collect, describe, display, manage and
facilitate semantic resource discovery, called EcoPortal. Based on OntoPortal, EcoPortal has
achieved the key functionality targets commonly expected by knowledge organisation system
repositories. In addition, it allows for resource updating through an integrated editor,
VocBench, while published resources may also obtain a Digital Object Identification for citing.
Keywords 1
Ecology, biodiversity, FAIR, semantic resource, knowledge organisation system, EcoPortal
1. Introduction
Perceiving the necessity for collaboration and integration to overcome fragmented and siloed
ecological data [1], research has been investing in creation and exploitation of semantic resources.
Formalised knowledge organisation systems (KOS) of a range of intricacy may now be encountered,
from simple lists of local species to domain thesauri, all aiming at systematising knowledge and aligning
information. With advancements in data collection and the accumulation of vast amounts of data to be
consumed, this need for homogeneity has nowadays become even more pressing [2].
To serve the purpose of knowledge integration, targets for data producers and publishers have been
summarised in the four main principles of FAIRness: Findability, Accessibility, Interoperability, and
Reusability [3]. For semantic resources, these principles have been translated into ten rules for accurate
communication across the users and producers of ecological information [4]. Among others, the rules
make it explicit that FAIR KOS be available from at least one repository recognised by the target
community, with adequate metadata, resource mappings, feedback mechanisms and proper citation.
This paper presents EcoPortal, a repository implemented to host KOS, promote discoverability,
render content and metadata accessible, increase interoperability, and facilitate reuse.
2. The EcoPortal environment
S4BioDiv 2021: 3rd International Workshop on Semantics for Biodiversity, held at JOWO 2021: Episode VII The Bolzano Summer of
Knowledge, September 11-18, 2021, Bolzano, Italy
EMAIL: xeni.kechagioglou@lifewatch.eu (X. Kechagioglou); pierfrancesco.tommasino@iret.cnr.it (P. Tommasino);
lucia.vaira@lifewatch.eu (L. Vaira); nicola.fiore@lifewatch.eu (N. Fiore); alberto.basset@lifewatch.eu (A. Basset); ilaria.rosati@cnr.it (I.
Rosati)
ORCID: 0000-0002-5935-6074 (L. Vaira); 0000-0002-9538-2966 (N. Fiore); 0000-0002-3603-9316 (A. Basset); 0000-0003-3422-7230 (I.
Rosati)
© 2021 Copyright for this paper by its authors.
Use permitted under Creative Commons License Attribution 4.0 International (CC BY 4.0).
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The initiative to implement a repository for ecological semantic resources was taken by LifeWatch
Italy and the Long-Term Ecosystem Research Network in Europe (LTER-Europe) [5]. The physical
realization of EcoPortal (ecoportal.lifewatch.eu) was launched by the European consortium for e-
science infrastructure for biodiversity and ecosystem research (LifeWatch ERIC). The domain niche
specified for the repository is ecology, particularly biodiversity and ecosystem research, as well as
biological and physical environmental data observations. It pertains all fields relevant to the study of
ecosystems, including both their biotic and abiotic components and their interactions.
Biodiversity is also a theme of interest to AgroPortal [6], although there it is intended as auxiliary
to the main domains: agronomy and plants. Similarly, the GFBio Terminology Service [7] lists largely
relevant KOS, although its thematic scope goes beyond that of EcoPortal, to include e.g., geosciences
and chemistry. The EcoPortal niche laps slightly over also with the repository of biomedical ontologies
BioPortal [8], whose collection includes a few KOS on phenotype, biotic and abiotic stress, and
organism diversity. This overlap of fields of interest is not a drawback. On the contrary, it may serve as
incentive for resource harmonization, development of cross-portal services and even detection of novel
affinities. Nor may it be foreseen to shrink; if anything, one may expect niche expansion for EcoPortal
to encompass new directions, as demonstrate indicative cases such as species conservation [9].
To meet the functional scope commonly expected by KOS repositories, and thus differentiate from
KOS registries that merely store and retrieve metadata about semantic assets [10], EcoPortal adheres to
a set of key functionalities specified in [11]. The main components of the EcoPortal environment are
the repository deployment infrastructure OntoPortal and the VocBench platform for semantic resource
development, both coming with compatibility with a Resource Description Framework (RDF) store.
2.1. Basic Functionalities
The basic functionalities of EcoPortal are based on OntoPortal (deployed version 2.5), a VMware
Virtual Appliance infrastructure [12] currently maintained by the Stanford Center for Biomedical
Informatics Research (BMIR). It is advanced by and for the collaborative OntoPortal Alliance [13], of
which LifeWatch ERIC is an active member. Its basic tools cater for browsing, searching, publishing,
annotating, mapping, and receiving recommendations for semantic assets.
Figure 1: The browsing interface of EcoPortal. Central to the view is the list of published KOS with an
indication of their size. Users may restrict their search by ecological categories (among others), and
they may also query the list by text.
Browse
Browsing (Figure 1) is assisted by matching user-inserted text to the title or the description of the
KOS. Filtering is accomplished by means of EcoPortal-specific categories (Table 1), currently mostly
coinciding with GEMET (GEneral Multilingual Environmental Thesaurus) concepts [14] and intended
to be updated according to user needs. Upon location of a KOS of interest, users may view its metadata,
as well as visualise its hierarchical and overall structure and content.
Table 1
EcoPortal categories for filtering the resources during browsing
Category Name Source Category Name Source Category Name Source
Ecology GEMET Biodiversity GEMET Earth sciences EcoPortal
Applied ecology GEMET Biodiversity GEMET Environmental EcoPortal
conservation sciences
Forest ecology GEMET Terrestrial GEMET Oceanography EcoPortal
biodiversity
Landscape GEMET Aquatic biodiversity GEMET
ecology
Plant ecology GEMET Urban biodiversity GEMET
Population GEMET Soil biodiversity GEMET
ecology
Synecology GEMET Forest biodiversity GEMET
Urban ecology GEMET Species diversity EcoPortal
Human ecology GEMET Ecosystem diversity EcoPortal
Animal ecology GEMET Functional diversity EcoPortal
Aquatic ecology GEMET Genetic diversity GEMET
Palaeoecology GEMET
Trophic ecology GEMET
Search, Mappings, Annotator, Recommender
Searching for specific concepts in the entire list of KOS also uses the above ecological categories to
filter results. Mapping of similar concepts across EcoPortal resources is based on text-matching concept
labels, while text analysis for annotation operates by string matching and by leveraging the KOS
hierarchical structure and mappings [15]. Equally important for resource reuse, the Recommender
service evaluates relevance of each EcoPortal KOS with regard to keywords or free text inserted by the
user. The tool builds on the annotation service, as well as on statistical and quality metrics of the
resources and of the annotation output, before assigning criteria weights and computing scores [16].
Publish
Publishing a new KOS on EcoPortal is at the heart of the repository’s existence. The resources have
metadata associated with them, submitted to the system through an online form upon uploading. The
required elements follow a schema (Table 2) that, having started with the BioPortal Metadata ontology
[17], was adjusted with elements from the extended AgroPortal schema [18] and was completed with
fields from the DataCite Metadata Schema (v.4.3) [19]. Albeit all elements were selected to serve
FAIRness, the DataCite ones in particular are meant for Digital Object Identifier (DOI) assignment to
the uploaded KOS.
Uploading of a KOS is not a prerequisite to its indexing in EcoPortal. In fact, the cataloguing aspect
of the repository is independent of whether the resource resides in it or not, as long as sufficient
information for successful redirection is provided. Uploaded resources may further be marked as public
or private, imposing restrictions on their accessibility, while persons indicated as contacts may
optionally receive feedback in the form of comments and proposals from users of their resource.
Table 2
The main metadata elements for KOS description in EcoPortal
Metadata element Description Source
Name Name of the KOS BioPortal
Acronym Acronym of the KOS BioPortal
Description Description of the KOS BioPortal
Status Release status, e.g., alpha BioPortal
Version KOS version AgroPortal
Format KOS format AgroPortal
Visibility Viewing restrictions (public/private) AgroPortal
Contact Name and e-mail of contact person AgroPortal
Homepage Homepage URL AgroPortal
Publications URL for bibliographic reference AgroPortal
Documentation URL for further documentation AgroPortal
Categories Controlled list with categories AgroPortal
Groups Controlled list with groups AgroPortal
Release date Date of upload to the EcoPortal AgroPortal
Identifier Unique string ID (e.g., DOI) DataCite
Identifier type Type of identifier DataCite
Creators Actors involved in KOS creation DataCite
Titles Alternative names of the KOS DataCite
Publisher Publishing entity DataCite
Resource type KOS type, e.g., ontology DataCite
Resource type general Dataset or other DataCite
2.2. EcoPortal extended functionalities
VocBench
Recognising the need for editing and updating EcoPortal resources with as few steps as possible, the
VocBench 3 (VB3) development platform has been integrated. VB3 - deployed version 8.02 - is an
open-source editing environment for ontologies, thesauri and RDF datasets. Initially created to support
the needs of the AGROVOC thesaurus, it offers itself as a web-based platform [20].
Connection between VocBench and EcoPortal user accounts is established via a personal API key
assigned to the user upon registration to EcoPortal. Users may update the resource in VocBench when
and as deemed suitable; once the new version is ready to be submitted in EcoPortal, users may do so
from VocBench, through a form (Figure 2) that contains the same metadata fields as the EcoPortal
Publish tool does; in this way, KOS deployment through VocBench automatically updates EcoPortal.
Beyond employing a straightforward process for new KOS versions, advantages to using VocBench
include better development control. Users assigned to a collaborative KOS creation project may be
delegated roles and get authorisation to perform specific tasks only, while all edits undergo a validation
process. Last, VocBench comes with a SPARQL endpoint for querying KOS structures and linked data.
Digital Object Identifier
LifeWatch ERIC is a direct member of DataCite and has the authorisation to provide a DOI to
ecological semantic resources that fulfil certain quality criteria, in order to be cited in a reliable and
constant way. KOS owners may request this upon publication of their resource on the EcoPortal
repository. DOI assignment is free of charge and is deemed fundamental to the FAIRness of resources.
Figure 2: The EcoPortal metadata schema for KOS description is respected whether resource
submission occurs through EcoPortal or through VocBench.
3. Conclusion and outlook
The EcoPortal environment for FAIR semantic resources in the ecological domain currently fulfils
functionalities commonly required by KOS repositories, while it also offers unique capabilities that
increase reuse of the hosted assets. Its realisation is incorporated in the broader mission of LifeWatch
ERIC to support with e-science infrastructure the scientific community in biodiversity and ecosystem
research. Next steps in its establishment involve cases of utilisation by the end users to guide
implementation of new repository features, as well as component upgrade and consolidation in a new
LifeWatch ERIC platform.
End users play in fact a key role in EcoPortal advancement, as identification of needs and design for
improvement may only be achieved through stepping-up the engagement of the ecological community
and the exchange of feedback. In this way, the EcoPortal environment may serve its purpose as the
entry point for KOS discovery, with the aim to use them in annotation of Digital Objects, in enrichment
of data, in reuse of information and services, and in FAIR maintenance of resources and components.
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