FAIR (meta)data presuppose their successful communication between machines and humans while preserving meaning and reference. The FAIR Guiding Principles lack specificity regarding semantic interoperability. We adopt a linguistic perspective on semantic interoperability and investigate the structures and conventions ensuring reliable communication of textual information, drawing parallels with data structures by understanding both as models. We propose a conceptual model of semantic interoperability, comprising intensional and extensional terminological interoperability, as well as logical and schema propositional interoperability. Since there cannot be a universally accepted best vocabulary and best (meta)data schema, establishing semantic interoperability necessitates the provision of comprehensive sets of intensional and extensional entity mappings and schema crosswalks. In accordance with our conceptual model, we suggest additions to the FAIR Guiding Principles that encompass the requirements for semantic interoperability. Additionally, we argue that attaining FAIRness of (meta)data requires not only their organization into FAIR Digital Objects, but also the establishment of a FAIR ecosystem of FAIR Services, that include a terminology, a schema, and an operations service.

Biodiversity research studies the variability and diversity of organisms, including variability within and between species with particular focus on the functional diversity of traits and their relationship to environment. Managing biodiversity data implies dealing with its heterogeneous nature using semantics and tailored ontologies. These are themselves differently conceived, and combining them in semantically enabled applications necessitates an effective alignment between their concepts. This paper describes the ontology matching of biodiversity- and ecology-related ontologies. We illustrate diverse challenges introduced by this kind of ontologies to ontology matching in general. Real use cases requiring pairwise alignments between environment and trait ontologies are introduced. We describe our experience creating a new track at the Ontology Alignment Evaluation Initiative designed for this specific domain and report on the results obtained by state-of-the-art participating systems. The biodiversity and ecology use case turns out to be a strong one for ontology matching, introducing new interesting challenges. Even if most of the matching systems perform relatively well in the proposed matching tasks, there is still room for improvement. We highlight possible directions in that matter and elaborate on our plan to further progress with the track.

Ontologies and knowledge graphs (KGs) are general-purpose computable representations of some domain, such as human anatomy, and are frequently a crucial part of modern information systems. Most of these structures change over time, incorporating new knowledge or information that was previously missing. Managing these changes is a challenge, both in terms of communicating changes to users and providing mechanisms to make it easier for multiple stakeholders to contribute. To fill that need, we have created KGCL, the Knowledge Graph Change Language (https://github.com/INCATools/kgcl), a standard data model for describing changes to KGs and ontologies at a high level, and an accompanying human-readable Controlled Natural Language (CNL). This language serves two purposes: a curator can use it to request desired changes, and it can also be used to describe changes that have already happened, corresponding to the concepts of “apply patch” and “diff” commonly used for managing changes in text documents and computer programs. Another key feature of KGCL is that descriptions are at a high enough level to be useful and understood by a variety of stakeholders—e.g. ontology edits can be specified by commands like “add synonym ‘arm’ to ‘forelimb’” or “move ‘Parkinson disease’ under ‘neurodegenerative disease’.” We have also built a suite of tools for managing ontology changes. These include an automated agent that integrates with and monitors GitHub ontology repositories and applies any requested changes and a new component in the BioPortal ontology resource that allows users to make change requests directly from within the BioPortal user interface. Overall, the KGCL data model, its CNL, and associated tooling allow for easier management and processing of changes associated with the development of ontologies and KGs. Database URL: https://github.com/INCATools/kgcl