Filters

2022 - 20242

More filters

2022 - 20242
Reset filters

Settings

End date: 2024 × Start date: 2021 × End date: 2024 × Start date: 2020 × DDC: 570 × DDC: 610 × Type: Text × Publisher: London : BioMed Central ×

Search Results

Now showing 1 - 2 of 2
  • Thumbnail Image
    Item
    Anatomy and the type concept in biology show that ontologies must be adapted to the diagnostic needs of research
    (London : BioMed Central, 2022) Vogt, Lars; Mikó, István; Bartolomaeus, Thomas
    Background: In times of exponential data growth in the life sciences, machine-supported approaches are becoming increasingly important and with them the need for FAIR (Findable, Accessible, Interoperable, Reusable) and eScience-compliant data and metadata standards. Ontologies, with their queryable knowledge resources, play an essential role in providing these standards. Unfortunately, biomedical ontologies only provide ontological definitions that answer What is it? questions, but no method-dependent empirical recognition criteria that answer How does it look? questions. Consequently, biomedical ontologies contain knowledge of the underlying ontological nature of structural kinds, but often lack sufficient diagnostic knowledge to unambiguously determine the reference of a term. Results: We argue that this is because ontology terms are usually textually defined and conceived as essentialistic classes, while recognition criteria often require perception-based definitions because perception-based contents more efficiently document and communicate spatial and temporal information—a picture is worth a thousand words. Therefore, diagnostic knowledge often must be conceived as cluster classes or fuzzy sets. Using several examples from anatomy, we point out the importance of diagnostic knowledge in anatomical research and discuss the role of cluster classes and fuzzy sets as concepts of grouping needed in anatomy ontologies in addition to essentialistic classes. In this context, we evaluate the role of the biological type concept and discuss its function as a general container concept for groupings not covered by the essentialistic class concept. Conclusions: We conclude that many recognition criteria can be conceptualized as text-based cluster classes that use terms that are in turn based on perception-based fuzzy set concepts. Finally, we point out that only if biomedical ontologies model also relevant diagnostic knowledge in addition to ontological knowledge, they will fully realize their potential and contribute even more substantially to the establishment of FAIR and eScience-compliant data and metadata standards in the life sciences.
  • Thumbnail Image
    Item
    Semantic units: organizing knowledge graphs into semantically meaningful units of representation
    (London : BioMed Central, 2024) Vogt, Lars; Kuhn, Tobias; Hoehndorf, Robert
    Background In today’s landscape of data management, the importance of knowledge graphs and ontologies is escalating as critical mechanisms aligned with the FAIR Guiding Principles—ensuring data and metadata are Findable, Accessible, Interoperable, and Reusable. We discuss three challenges that may hinder the effective exploitation of the full potential of FAIR knowledge graphs. Results We introduce “semantic units” as a conceptual solution, although currently exemplified only in a limited prototype. Semantic units structure a knowledge graph into identifiable and semantically meaningful subgraphs by adding another layer of triples on top of the conventional data layer. Semantic units and their subgraphs are represented by their own resource that instantiates a corresponding semantic unit class. We distinguish statement and compound units as basic categories of semantic units. A statement unit is the smallest, independent proposition that is semantically meaningful for a human reader. Depending on the relation of its underlying proposition, it consists of one or more triples. Organizing a knowledge graph into statement units results in a partition of the graph, with each triple belonging to exactly one statement unit. A compound unit, on the other hand, is a semantically meaningful collection of statement and compound units that form larger subgraphs. Some semantic units organize the graph into different levels of representational granularity, others orthogonally into different types of granularity trees or different frames of reference, structuring and organizing the knowledge graph into partially overlapping, partially enclosed subgraphs, each of which can be referenced by its own resource. Conclusions Semantic units, applicable in RDF/OWL and labeled property graphs, offer support for making statements about statements and facilitate graph-alignment, subgraph-matching, knowledge graph profiling, and for management of access restrictions to sensitive data. Additionally, we argue that organizing the graph into semantic units promotes the differentiation of ontological and discursive information, and that it also supports the differentiation of multiple frames of reference within the graph.