1,877 research outputs found
The Role of Foundational Relations in the Alignment of Biomedical Ontologies
The Foundational Model of Anatomy (FMA) symbolically represents the structural organization of the human body from the macromolecular to the macroscopic levels, with the goal of providing a robust and consistent scheme for classifying anatomical entities on the basis of explicit definitions. This scheme also provides a template for modeling pathology, physiological function and genotype-phenotype correlations, and it can thus serve as a reference ontology in biomedical informatics. Here we articulate the need for formally clarifying the is-a and partof relations in the FMA and similar ontology and terminology systems. We diagnose certain characteristic errors in the treatment of these relations and show how these errors can be avoided through adoption of the formalism we describe. We then illustrate how a consistently applied formal treatment of taxonomy and partonomy can support the alignment of ontologies
The Foundational Model of Anatomy Ontology
Anatomy is the structure of biological organisms. The term also denotes the scientific
discipline devoted to the study of anatomical entities and the structural and
developmental relations that obtain among these entities during the lifespan of an
organism. Anatomical entities are the independent continuants of biomedical reality on
which physiological and disease processes depend, and which, in response to etiological
agents, can transform themselves into pathological entities. For these reasons, hard copy
and in silico information resources in virtually all fields of biology and medicine, as a
rule, make extensive reference to anatomical entities. Because of the lack of a
generalizable, computable representation of anatomy, developers of computable
terminologies and ontologies in clinical medicine and biomedical research represented
anatomy from their own more or less divergent viewpoints. The resulting heterogeneity
presents a formidable impediment to correlating human anatomy not only across
computational resources but also with the anatomy of model organisms used in
biomedical experimentation. The Foundational Model of Anatomy (FMA) is being
developed to fill the need for a generalizable anatomy ontology, which can be used and
adapted by any computer-based application that requires anatomical information.
Moreover it is evolving into a standard reference for divergent views of anatomy and a
template for representing the anatomy of animals. A distinction is made between the FMA
ontology as a theory of anatomy and the implementation of this theory as the FMA
artifact. In either sense of the term, the FMA is a spatial-structural ontology of the
entities and relations which together form the phenotypic structure of the human
organism at all biologically salient levels of granularity. Making use of explicit
ontological principles and sound methods, it is designed to be understandable by human
beings and navigable by computers. The FMA’s ontological structure provides for
machine-based inference, enabling powerful computational tools of the future to reason
with biomedical data
Infectious Disease Ontology
Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain
Anatomical information science
The Foundational Model of Anatomy (FMA) is a map of the human body. Like maps of other sorts – including the map-like representations we find in familiar anatomical atlases – it is a representation of a certain portion of spatial reality as it exists at a certain (idealized) instant of time. But unlike other maps, the FMA comes in the form of a sophisticated ontology of its objectdomain, comprising some 1.5 million statements of anatomical relations among some 70,000 anatomical kinds. It is further distinguished from other maps in that it represents not some specific portion of spatial reality (say: Leeds in 1996), but rather the generalized or idealized spatial reality associated with a generalized or idealized human being at some generalized or idealized instant of time. It will be our concern in what follows to outline the approach to ontology that is represented by the FMA and to argue that it can serve as the basis for a new type of anatomical information science. We also draw some implications for our understanding of spatial reasoning and spatial ontologies in general
The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration
The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies, which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform, and new ontologies being created, on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved in the future
Desiderata for domain reference ontologies in biomedicine
AbstractDomain reference ontologies represent knowledge about a particular part of the world in a way that is independent from specific objectives, through a theory of the domain. An example of reference ontology in biomedical informatics is the Foundational Model of Anatomy (FMA), an ontology of anatomy that covers the entire range of macroscopic, microscopic, and subcellular anatomy. The purpose of this paper is to explore how two domain reference ontologies—the FMA and the Chemical Entities of Biological Interest (ChEBI) ontology, can be used (i) to align existing terminologies, (ii) to infer new knowledge in ontologies of more complex entities, and (iii) to manage and help reasoning about individual data. We analyze those kinds of usages of these two domain reference ontologies and suggest desiderata for reference ontologies in biomedicine. While a number of groups and communities have investigated general requirements for ontology design and desiderata for controlled medical vocabularies, we are focusing on application purposes. We suggest five desirable characteristics for reference ontologies: good lexical coverage, good coverage in terms of relations, compatibility with standards, modularity, and ability to represent variation in reality
Foundational Ontologies meet Ontology Matching: A Survey
Ontology matching is a research area aimed at finding ways to make different ontologies interoperable. Solutions to the problem have been proposed from different disciplines, including databases, natural language processing, and machine learning. The role of foundational ontologies for ontology matching is an important one. It is multifaceted and with room for development. This paper presents an overview of the different tasks involved in ontology matching that consider foundational ontologies. We discuss the strengths and weaknesses of existing proposals and highlight the challenges to be addressed in the future
A formal theory for spatial representation and reasoning in biomedical ontologies
Objective: The objective of this paper is to demonstrate how a
formal spatial theory can be used as an important tool for
disambiguating the spatial information embodied in biomedical
ontologies and for enhancing their automatic reasoning capabilities.
Method and Materials: This paper presents a formal theory of parthood
and location relations among individuals, called Basic Inclusion
Theory (BIT). Since biomedical ontologies are comprised of assertions
about classes of individuals (rather than assertions about individuals),
we define parthood and location relations among classes in the
extended theory BIT+Cl (Basic Inclusion Theory for Classes). We
then demonstrate the usefulness of this formal theory for making
the logical structure of spatial information more precise in two
ontologies concerned with human anatomy: the Foundational Model of
Anatomy (FMA) and GALEN.
Results: We find that in both the FMA and GALEN, class-level spatial
relations with different logical properties are not always explicitly
distinguished. As a result, the spatial information included in
these biomedical ontologies is often ambiguous and the possibilities
for implementing consistent automatic reasoning within or across
ontologies are limited.
Conclusion: Precise formal characterizations of all spatial relations
assumed by a biomedical ontology are necessary to ensure that the
information embodied in the ontology can be fully and coherently
utilized in a computational environment. This paper can be seen as
an important beginning step toward achieving this goal, but much
more work is along these lines is required
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