Harnessing the Power of Unified Metadata in an Ontology Repository: The Case of AgroPortal

Abstract

As any resources, ontologies, thesaurus, vocabularies and terminologies need to be described with relevant metadata to facilitate their identification, selection and reuse. For ontologies to be FAIR, there is a need for metadata authoring guidelines and for harmonization of existing metadata vocabularies-taken independently none of them can completely describe an ontology. Ontology libraries and repositories also have to play an important role. Indeed, some metadata properties are intrinsic to the ontology (name, license, description); other information, such as community feedbacks or relations to other ontologies are typically information that an ontology library shall capture, populate and consolidate to facilitate the processes of identifying and selecting the right ontology(ies) to use. We have studied ontology metadata practices by: (1) analyzing metadata annotations of 805 ontologies; (2) reviewing the most standard and relevant vocabularies (23 totals) currently available to describe metadata for ontologies (such as Dublin Core, Ontology Metadata Vocabulary, VoID, etc.); (3) comparing different metadata implementation in multiple ontology libraries or repositories. We have then built a new metadata model for our AgroPortal vocabulary and ontology repository, a platform dedicated to agronomy based on the NCBO BioPortal technology. AgroPortal now recognizes 346 properties from existing metadata vocabularies that could be used to describe different aspects of ontologies: intrinsic descriptions, people, date, relations, content, metrics, community, administration, and access. We use them to populate an internal model of 127 properties implemented in the portal and harmonized for all the ontologies. We-and AgroPortal's users-have spent a significant amount of time to edit and curate the metadata of the ontologies to offer a better synthetized and harmonized information and enable new ontology identification features. Our goal was also to facilitate the comprehension of the agronomical ontology landscape by displaying diagrams and charts about all the ontologies on the portal. We have evaluated our work with a user appreciation survey which confirms the new features are indeed relevant and helpful to ease the processes of identification and selection of ontologies. This paper presents how to harness the potential of a complete and unified metadata model with dedicated features in an ontology repository; however, the new AgroPortal's model is not a new vocabulary as it relies on preexisting ones. A generalization of this work is studied in a community-driven standardization effort in the context of the RDA Vocabulary and Semantic Services Interest Group.

39 Hints to Facilitate the Use of Semantics for Data on Agriculture and Nutrition

“…Based on the consideration that semantics is ubiquitous in tasks involving data, the group investigated the status of formal semantic resources for the agriculture domain. To this end, we used: a "Map of data standards for food and agriculture" (from now on "the Map") corresponding to a catalog of SRs and standards that later became the "Agrisemantics Map of Data Standards" (Pesce et al, 2018), and the AgroPortal vocabulary and ontology repository (Jonquet et al, 2018b(Jonquet et al, , 2018a. To the best of our knowledge, the Map and AgroPortal are the only initiatives specifically addressing the agrifood domain.…”

“…AgroPortal is a public repository of semantic resources (AgroPortal, release 2.0, Sept. 2020; Jonquet et al, 2018bJonquet et al, , 2018a reusing the NCBO BioPortal technology (Noy et al, 2009), and offering ontology hosting, search, versioning, visualization, comment and recommendation. It enables semantic annotation and supports basic alignment features via a user web interface and web services.…”

“…Specific agrifood communities (e.g., INRAE, Crop Ontology project, RDA WDI WG) are supported with customized facilities, such as SR grouping and interfaces (R19). 11 AgroPortal supports SR developers in using a unified metadata model based on a shared specification (MOD 1.4 (Jonquet et al, 2018b)) (R3) and, when available, metadata can also be automatically generated (R6). AgroPortal's SR metadata are mainly used to: (i) serve as a means to create connections to other existing catalogs, libraries and repositories (FAIRsharing, OBO Foundry, Ontobee, etc.)…”

Recommendations for the FAIRification of genomic track metadata

“…FAIRsharing lvi annotates ontologies with richer metadata and provides a better experience for discovering ontologies. The AgroPortal 29 provides an expressive search interface built on a general model created by merging standards for metadata on ontologies, but the portal only supports ontologies in agronomy and related domains. In practice, we chose ontologies manually by getting an impression by searching for key terms, using e.g.…”

OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies

“…In the more general domain of linked data, there is also the Vocabulary of a Friend, which allows for the description of inter-vocabulary relationships ( 6 ). More recently, AgroPortal studied common metadata practices and used their results to build a new metadata model that harmonized these existing practices ( 7 ). Finally, Matentzoglu et al.…”