A Fourfold Pathogen Reference Ontology Suite

Infectious diseases remain a critical global health challenge, and the integration of standardized ontologies plays a vital role in managing related data. The Infectious Disease Ontology (IDO) and its extensions, such as the Coronavirus Infectious Disease Ontology (CIDO), are essential for organizing and disseminating information related to infectious diseases. The COVID-19 pandemic highlighted the need for updating IDO and its virus-specific extensions. There is an additional need to update IDO extensions specific to bacteria, fungus, and parasite infectious diseases. We adopt the "hub and spoke" methodology to generate pathogen-specific extensions of IDO: Virus Infectious Disease Ontology (VIDO), Bacteria Infectious Disease Ontology (BIDO), Mycosis Infectious Disease Ontology (MIDO), and Parasite Infectious Disease Ontology (PIDO). The creation of pathogen-specific reference ontologies advances modularization and reusability of infectious disease data within the IDO ecosystem. Future work will focus on further refining these ontologies, creating new extensions, and developing application ontologies based on them, in line with ongoing efforts to standardize biological and biomedical terminologies for improved data sharing and analysis.

Mapping the Provenance Ontology to Basic Formal Ontology

The Provenance Ontology (PROV-O) is a World Wide Web Consortium (W3C) recommended ontology used to structure data about provenance across a wide variety of domains. Basic Formal Ontology (BFO) is a top-level ontology ISO/IEC standard used to structure a wide variety of ontologies, such as the OBO Foundry ontologies and the Common Core Ontologies (CCO). To enhance interoperability between these two ontologies, their extensions, and data organized by them, an alignment is presented according to a specific mapping criteria and methodology which prioritizes structural and semantic considerations. The ontology alignment is evaluated by checking its logical consistency with canonical examples of PROV-O instances and querying terms that do not satisfy the mapping criteria as formalized in SPARQL. A variety of semantic web technologies are used in support of FAIR (Findable, Accessible, Interoperable, Reusable) principles.

Towards a Cyber Information Ontology

This paper introduces a set of terms that are intended to act as an interface between cyber ontologies (like a file system ontology or a data fusion ontology) and top- and mid-level ontologies, specifically Basic Formal Ontology and the Common Core Ontologies. These terms center on what makes cyberinformation management unique: numerous acts of copying items of information, the aggregates of copies that result from those acts, and the faithful members of those aggregates that represent all other members.

Foundations for Digital Twins

The growing reliance on digital twins across various industries and domains brings with it semantic interoperability challenges. Ontologies are a well-known strategy for addressing such challenges, though given the complexity of the phenomenon, there are risks of reintroducing the interoperability challenges at the level of ontology representations. In the interest of avoiding such pitfalls, we introduce and defend characterizations of digital twins within the context of the Common Core Ontologies, an extension of the widely-used Basic Formal Ontology. We provide a set of definitions and design patterns relevant to the domain of digital twins, highlighted by illustrative use cases of digital twins and their physical counterparts. In doing so, we provide a foundation on which to build more sophisticated ontological content related and connected to digital twins.

Grounding Realizable Entities

Ontological representations of qualities, dispositions, and roles have been refined over the past decade, clarifying subtle distinctions in life science research. After articulating a widely-used characterization of these entities within the context of Basic Formal Ontology (BFO), we identify gaps in this treatment and motivate the need for supplementing the BFO characterization. By way of supplement, we propose definitions for grounding relations holding between qualities and dispositions, and dispositions and roles, illustrating our proposal by representing subtle aspects of host-pathogen interactions.

Credentials in the Occupation Ontology

The term credential encompasses educational certificates, degrees, certifications, and government-issued licenses. An occupational credential is a verification of an individuals qualification or competence issued by a third party with relevant authority. Job seekers often leverage such credentials as evidence that desired qualifications are satisfied by their holders. Many U.S. education and workforce development organizations have recognized the importance of credentials for employment and the challenges of understanding the value of credentials. In this study, we identified and ontologically defined credential and credential-related terms at the textual and semantic levels based on the Occupation Ontology (OccO), a BFO-based ontology. Different credential types and their authorization logic are modeled. We additionally defined a high-level hierarchy of credential related terms and relations among many terms, which were initiated in concert with the Alabama Talent Triad (ATT) program, which aims to connect learners, earners, employers and education/training providers through credentials and skills. To our knowledge, our research provides for the first time systematic ontological modeling of the important domain of credentials and related contents, supporting enhanced credential data and knowledge integration in the future.

Capabilities

In our daily lives, as in science and in all other domains, we encounter huge numbers of dispositions (tendencies, potentials, powers) which are realized in processes such as sneezing, sweating, shedding dandruff, and on and on. Among this plethora of what we can think of as mere dispositions is a subset of dispositions in whose realizations we have an interest a car responding well when driven on ice, a rabbits lungs responding well when it is chased by a wolf, and so on. We call the latter capabilities and we attempt to provide a robust ontological account of what capabilities are that is of sufficient generality to serve a variety of purposes, for example by providing a useful extension to ontology-based research in areas where capabilities data are currently being collected in siloed fashion.

Middle Architecture Criteria

Mid-level ontologies are used to integrate terminologies and data across disparate domains. There are, however, no clear, defensible criteria for determining whether a given ontology should count as mid-level, because we lack a rigorous characterization of what the middle level of generality is supposed to contain. Attempts to provide such a characterization have failed, we believe, because they have focused on the goal of specifying what is characteristic of those single ontologies that have been advanced as mid-level ontologies. Unfortunately, single ontologies of this sort are generally a mixture of top- and mid-level, and sometimes even of domain-level terms. To gain clarity, we aim to specify the necessary and sufficient conditions for a collection of one or more ontologies to inhabit what we call a mid-level architecture.

The Common Core Ontologies

The Common Core Ontologies (CCO) are designed as a mid-level ontology suite that extends the Basic Formal Ontology. CCO has since been increasingly adopted by a broad group of users and applications and is proposed as the first standard mid-level ontology. Despite these successes, documentation of the contents and design patterns of the CCO has been comparatively minimal. This paper is a step toward providing enhanced documentation for the mid-level ontology suite through a discussion of the contents of the eleven ontologies that collectively comprise the Common Core Ontology suite.