Physical processes, their life and their history

Here, I lay the foundations of a high-level ontology of particulars whose structuring principles differ radically from the 'continuant' vs. 'occurrent' distinction traditionally adopted in applied ontology. These principles are derived from a new analysis of the ontology of “occurring” or “happening” entities. Firstly, my analysis integrates recent work on the ontology of processes, which brings them closer to objects in their mode of existence and persistence by assimilating them to continuant particulars. Secondly, my analysis distinguishes clearly between processes and events, in order to make the latter abstract objects of thought (alongside propositions). Lastly, I open my ontological inventory to properties and facts, the existence of which is commonly admitted. By giving specific roles to these primitives, the framework allows one to account for static and dynamic aspects of the physical world and for the way that subjects conceive its history: facts account for the life of substances (physical objects and processes), whereas events enable cognitive subjects to account for the life story of substances

Grid Metadata Lifetime Control in ActOn

In the Semantic Grid, metadata, as first class citizens, should be maintained up to-date in a cost-effective manner. This includes maxi missing the automation of different aspects of the metadata lifecycle, managing the evolution and change of metadata in distributed contexts, and synchronizing adequately the evolution of all these related entities. In this paper, we introduce a semantic model and its operations which is designed for supporting dynamic metadata management in Active Ontology (Act On), a semantic information integration approach for highly dynamic information sources. Finally, we illustrate the Act On-based metadata lifetime control by EGEE examples

How similar are objects and events?

Semanticists often assume an ontology for natural language that includes not only ordinary objects, but also events, and other sorts of entities. We link this ontology to how speakers represent static and dynamic entities. Specifically, we test how speakers determine whether an entity counts as “atomic” by using count vs. mass (e.g., some gleebs, some gleeb) and distributive vs. non-distributive descriptions (e.g., gleeb every second or so, gleeb around a little). We then seek evidence for atomic representation in a non-linguistic task. Ultimately we suggest that natural language ontology reveals properties of language-independent conceptualization

Web Ontologies as Renewal of Classical Philosophical Ontology

International audienceDo Web devices (addresses, tags, networks, and the rest) have counterparts in classical ontology? Yes, but they allow us also to introduce more refined distinctions. In addition, their dynamic use could inspire a dynamic reconception of classical ontology. In the process of making explicit ontological types, different types can be undistinguished as first steps (considered as "floating types") to be defined only in a further step, one in which their function as distinguishers of other kinds of entities has to be made explicit. The fact that the ontological import of some node in a network of tags and addresses could evolve with the transformation of the network can most easily find an interpretation in this dynamic conception of ontology

A pattern-based approach to a cell tracking ontology

Time-lapse microscopy has thoroughly transformed our understanding of biological motion and developmental dynamics from single cells to entire organisms. The increasing amount of cell tracking data demands the creation of tools to make extracted data searchable and interoperable between experiment and data types. In order to address that problem, the current paper reports on the progress in building the Cell Tracking Ontology (CTO): An ontology framework for describing, querying and integrating data from complementary experimental techniques in the domain of cell tracking experiments. CTO is based on a basic knowledge structure: the cellular genealogy serving as a backbone model to integrate specific biological ontologies into tracking data. As a first step we integrate the Phenotype and Trait Ontology (PATO) as one of the most relevant ontologies to annotate cell tracking experiments. The CTO requires both the integration of data on various levels of generality as well as the proper structuring of collected information. Therefore, in order to provide a sound foundation of the ontology, we have built on the rich body of work on top-level ontologies and established three generic ontology design patterns addressing three modeling challenges for properly representing cellular genealogies, i.e. representing entities existing in time, undergoing changes over time and their organization into more complex structures such as situations

Biological taxonomy and ontology development: scope and limitations

The prospects of integrating full-blown biological taxonomies into an ontological reasoning framework are reviewed. We contrast the common usage of a static 'snapshot' hierarchy in ontological representations of taxonomy with a more realistic situation that involves dynamic, piece-meal revisions of particular taxonomic groups and requires alignment with relevant preceding perspectives. Taxonomic practice is characterized by a range of phenomena that are orthogonal to the logical semantic background from which ontological entities and relationships originate, and therefore pose special challenges to ontological representation and reasoning. Among these phenomena are: (1) the notion that there is a single phylogenetic hierarchy in nature which taxonomy can only gradually approximate; (2) the evolvability of taxa which means that taxon-defining features may be lost in subordinate members or independently gained across multiple sections of the tree of life; (3) the hybrid approach of defining taxa both in reference to properties (intensional) and members (ostensive) which undermines the individual/class dichotomy sustaining conventional ontologies; (4) the idiosyncratic yet inferentially valuable usage of Linnaean ranks; (5) the indelible and semantically complex 250-year legacy of nomenclatural and taxonomic changes that characterizes the current system; (6) the insufficient taxonomic exploration of large portions of the tree of life; and the need to use a sophisticated terminology for aligning taxonomic entities in order to integrate both (7) single and (8) multiple hierarchies. We briefly such how such integration may proceed based on an initial expert alignment of concept relationship and subsequent use of first-order logic algorithms to maximize consistency, reveal implied relationships, and ultimately merge taxonomies.
 In light of the aforementioned obstacles, we suggest that research along the taxonomy/ontology interface should focus on either strictly nomenclatural entities or specialize in ontology-driven methods for producing alignments between multiple taxonomies. We furthermore suggest that the prospects of developing successful ontologies for taxonomy will largely depend on the ability of the taxonomic expert community to present their phylogenies and classifications in a way that is more compatible with ontological reasoning than concurrent practice. Minimally, this means (1) adopting rigorous standards for linking new core taxonomies to relevant peripheral taxonomies through comprehensive alignments so that their ontological/taxonomic connections are transparent; (2) using lineage-specific ontological standards for phenotype-based accounts of taxa while taking into account the phylogenetic contextuality of phenotypic descriptors; (3) presenting all nomenclatural and taxonomic novelties in an explicit, ontology-compatible format, including intensional and ostensive definitions; and (4) offering comprehensive intensional/ostensive alignments to entities in relevant preceding taxonomies

Processes endure, whereas events occur

In this essay, we aim to help clarify the nature of so-called 'occurrences' by attributing distinct modes of existence and persistence to processes and events. In doing so, we break with the perdurantism claimed by DOLCE’s authors and we distance ourselves from mereological analyzes like those recently conducted by Guarino to distinguish between 'processes' and 'episodes'. In line with the works of Stout and Galton, we first bring closer (physical) processes and objects in their way of enduring by proposing for processes a notion of dynamic presence (contrasting with a static presence for objects). Then, on the events side, we attribute to them the status of abstract entities by identifying them with objects of thought (by individual and collective subjects), and this allows us to distinguish for themselves between existence and occurrence. We therefore identify them with psychological (or even social) endurants, which may contingently occur