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Ebook: Formal Ontology in Information Systems
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The complex information systems which have evolved in recent decades rely on robust and coherent representations in order to function. Such representations and associated reasoning techniques constitute the modern discipline of formal ontology, which is now applied to fields such as artificial intelligence, computational linguistics, bioinformatics, GIS, conceptual modeling, knowledge engineering, information retrieval, and the semantic web. Ontologies are increasingly employed in a number of complex real-world application domains. For instance, in biology and medicine, more and more principle-based ontologies are being developed for the description of biological and biomedical phenomena. To be effective, such ontologies must work well together, and as they become more widely used, achieving coordinated development presents a significant challenge. This book presents collected articles from the 7th International Conference on Formal Ontologies (FOIS), held in Graz, Austria, in July 2012. FOIS is a forum which brings together representatives of all major communities involved in the development and application of ontologies to explore both theoretical issues and concrete applications in the field. The book is organized in eight sections, each of which deals with the ontological aspects of: bioinformatics; physical entities; artifacts and human resources; ontology evaluation; language and social relations; time and events; representation and the methodological aspects of ontological engineering. Providing a current overview of developments in formal ontology, this book will be of interest to all those whose work involves the application of ontologies, and to anybody wishing to keep abreast of advances in the field.
This volume collects articles presented at the 7th edition of the International Conference on Formal Ontologies in Information Systems (FOIS 2012). This edition of this bi-annual conference was held in conjunction with with the 3rd edition of the International Conference on Biomedical Ontologies (ICBO 2012), in Graz, Austria.
We received 71 submissions from all continents, in particular, from authors affiliated with institutions in countries such as Algeria, Australia, Austria, Brazil, Canada, China, France, Germany, Hong Kong, Ireland, Italy, Japan, Mexico, Norway, Poland, Russia, Senegal, Singapore, South Africa, Spain, Sweden, Switzerland, Taiwan, Thailand, United States and United Kingdom. All submissions were carefully reviewed by the members of our international program committee. Based on the reviews, 24 articles were chosen for presentation at the conference. Accepted submissions were organized into 8 sessions: Ontologies and Bioinformatics; Ontologies of Physical Entities; Ontological Aspects of Artifacts and Human Resources; Methodological Aspects of Ontological Engineering; Ontology Evaluation; Ontology, Language and Social Relations; Ontological Aspects of Time and Events; Aspects of Ontology Representation. The wide range of topics addressed in these sessions demonstrates that formal ontology is an active area of research which addresses problems ranging from theoretical questions regarding the ontology of time to the applications in the sciences and engineering.
Ontologies and Bioinformatics: in the first paper in this session entitled Probability assignments to dispositions in ontologies, Adrien Barton, Anita Burgun and Régis Duvauferrier investigate the probabilistic dimension of dispositions, with a particular interest on Biomedical ontologies. The authors investigate the determination of which kinds of dispositional entities (individuals, universals, both) a probability value can be assigned to; in Maturation of Neuroscience Information Framework: An Ontology Driven Information System for Neuroscience, Fahim T. Imam and colleagues discuss the main ontology-based components of the Neuroscience Information Framework (NIF). In the context of the NIF project, the ultimate end product is a semantic search engine and knowledge discovery portal that provides federated access to a vast amount of Neuroscience data and resources over the web. Finally, in Suggestions for Galaxy Workflow Design Using Semantically Annotated Services, Alok Dhamanaskar and colleagues propose an extension of the Galaxy open-source web-based framework to assist the user in the construction of Service-based Scientific Workflows. The work is based on proposed extensions to the Ontology for Biomedical Investigations (OBI) which are intended to provide a base for the semantic annotation of Web Services.
Ontologies of Physical Entities: in The Void in Hydro Ontology, Torsten Hahmann and Boyan Brodaric extend the DOLCE foundational ontology to a logical theory aimed at representing specific aspects of the physical containment of water studied in hydrology. More specifically, they address the notion of void – empty spaces that can be filled with water; in The mysterious appearance of objects, Emanuele Bottazzi, Ro berta Ferrario and Claudio Masolo present a constructivist approach to objects. This approach aims at making explicit how objects can be constructed as from the outcome of an apparatus, being it a measurement instrument or our perceptual system, discuss ing what are the ontological and representational problems faced by such an approach; finally, in Towards Making Explicit the Ontological Commitment of a Database Schema on the Geological Domain, Alda Maria Ferreira Rosa da Silva and Maria Cláudia Cavalcanti propose an approach which combines a set of reverse engineering techniques and the use of a top-level ontology as a way of making explicit the ontological commitment of a conceptual database schema. The proposal combines the OntoClean methodology and the OntoUML meta-categorization in a set of methodological guidelines aimed at producing higher-quality models to support tasks of interoperability and database integration.
Ontological Aspects of Artifacts and Human Resources: In the paper entitled An Ontology for Skill and Competency Management, Maryam Fazel-Zarandi and Mark S. Fox present a formal PSL-based ontology for representing, inferring, and validating skills and competencies of Human Resources in a dynamic environment; in Towards A Unified Definition of Function, Riichiro Mizoguchi, Yoshinobu Kitamura and Stefano Borgo build on an existing ontological definition of Artifact Functions, generalizing this notion to provide a general unified definition of functions aimed at characterizing both Biological Organisms and Technical Artifacts. Finally, in Preliminaries to a formal ontology of failure of engineering artifacts, Luca Del Frate advances a conceptual analysis of the notion of failure in engineering. The paper propose three different notion of failures which are intended to capture practitioners' intuitions and are advocated as an important step towards the definition of a formal ontology of failure.
Methodological Aspects in Ontology Engineering: In the paper entitled A method for re-engineering a thesaurus into an ontology, Daniel Kless and colleagues present a general method for re-engineering a standard-compliant thesaurus into an ontology by making use of top-level ontologies; In Ontology Content “At A Glance”, Gökhan Coskun, Mario Rothe and Adrian Paschke present a technique to group concepts for ontology documentation by applying community detection algorithms on the graph structure of ontologies. Finally, we have in this session Interactive Semantic Feedback for Intuitive Ontology Authoring by Ronald Denaux and colleagues. Their proposal aims at increasing the efficiency and effectiveness of the ontology authoring process by providing interactive, semantic feedback that helps ontology authors to consider relevant logical consequences of their modeling inputs.
Ontology Evaluation: in Does your ontology make a (sense) difference?, Pawel Garbacz proposes three logical criteria that an Applied Ontology need to satisfy in order to suitably achieve the task of satisfactorily characterize its terminology. These logical criteria correlate to graded levels of semantic indeterminacy. In sequence, we have two papers by A. Patrice Seyed. In the first of these papers, entitled A Method for Evaluating Ontologies Introducing the BFO-Rigidity Decision Tree Wizard, the author proposes an integration of OntoClean's notion of Rigidity with the BFO theory of types to provide a tool-supported decision tree procedure for evaluating ontologies. Moreover, in Integrating OntoClean's Notion of Unity and Identity with a Theory of Classes and Types: Towards a Method for Evaluating Ontologies, the author provides a reformulation of OntoClean's notion of Identity and Unity within a formal theory of classes and evaluates how the reformulations apply to BFO's theory of types. This work is aimed at making an additional contribution to ongoing efforts to build automated support to evaluate and standardize OBO Foundry candidate ontologies.
Ontology, Language and Social Relations: in Axiomatizing Change-of-State Words, Niloofar Montazeri and Jerry R. Hobbs present a part of their program of developing core theories of fundamental commonsense phenomena. These theories are then employed to define English word senses by means of axioms using predicates explicated in these theories. In particular, in this paper they focus on structure of events and, more specifically, on the axiomatization of on change-of-state words from the Core Wordnet; in Elements for a linguistic ontology in the verbal domain, Lucia M. Tovena discusses elements of a linguistically-motivated ontology and proposes a novel analysis to the philosophical notion of sortal in order to address aspects of essence and discretization of events; in Toward a Commonsense Theory of Microsociology: Interpersonal Relationships, Jerry R. Hobbs, Alicia Sagae and Suzanne Wertheim present a part of a formal ontology of microsociology (focused on small-scale social groups). The discussed part focuses on interpersonal relationships addressing concepts such as commitments, shared plans and good will and aimed at formally characterizing relationships such as the host-guest relationship and friendship in order to support inter-cultural communication.
Ontological Aspects of Time and Events: in The Data-Time Vocabulary, Mark H. Linehan, Ed Barkmeyer, and Stan Hendryx present a new OMG specification that models a Foundational Vocabulary of Time and related notions (e.g., continuous time, discrete time, the relationship of events and situations to time, language tense and aspect, time indexicals, timetables, and schedules). The proposal offers a linguistic-oriented vocabulary and ontology intended for supporting the specification of business rules in different business domains; in States, Processes and Events, and the Ontology of Causal Relations, Anthony Galton elaborates on the difficult subject of causation by advancing aspects of an ontology of particulars. This ontology elaborates on notions such as events, states and processes (taking a particular view on the latter two) as well as different causal and causal-like relations (e.g., initiation, termination, perpetuation, enablement and prevention) holding among them; Finally, in Ontology of Time in GFO, Ringo Baumann, Frank Loebe, and Heinrich Herre present a novel formal ontology of time as a part of the GFO research program. Besides presenting this formal theory, the authors revisit a number of problematic cases related to temporal representation and reasoning. Finally, a metalogical analysis for this theory is presented (including consistency, completeness and decidability results).
Aspects of Ontology Representation: in Using Partial Automorphisms to Design Process Ontologies, Bahar Aameri proposes a methodology for the design and verification of domain-specific process ontologies that are extensions of generic process ontologies by using the notion of partial automorphism (a mapping from a model to itself which preserves some substructures of the model); in A Temporal Extension of the Hayes/ter Horst Entailment Rules and an Alternative to W3C's N-ary Relations, Hans-Ulrich Krieger propose a novel approach that contains extended entailment rules for RDFS and the OWL Horst dialect and is designed to efficiently support encoding of temporally changing information in OWL and RDF; finally, in Three Semantics for the Core of the Distributed Ontology Language, Till Mossakowski, Christoph Lange and Oliver Kutz present the abstract syntax and new? kind of semantics for the meta-level constructs of the DOL (Distributed Ontology Language). A DOL Ontology consists of modules formalized in existing ontology languages (e.g., OWL, Common Logic, F-Logic). The language meta-level constructs can be employed to express different types of links between these heterogeneous ontologies.
As program chairs we would like to thank all of the authors who submitted their work and the reviewers who helped us to select the best papers from a pool of high quality submissions.
We investigate how probabilities can be assigned to dispositions in ontologies, building on Popper's propensity approach. We show that if D is a disposition universal associated with a trigger T and a realization R, and d is an instance of D, then one can assign a probability to the triplets (d,T,R) and (D,T,R). These probabilities measure the causal power of dispositions, which can be defined as limits of relative frequencies of possible instances of T triggering an instance of R over a hypothetical infinite random sequence of possible instances of T satisfying certain conditions. Adopting a fallibilist methodology, these probability values can be estimated by relative frequencies in actual finite sequences.
The numbers of available neuroscience resources (databases, tools, materials and networks) on the web have, and continue to expand; particularly in light of newly implemented data sharing policies required by funding agencies and journals. However, the nature of dense, multi-faceted neuroscience data and the design of classic search engine systems makes efficient, reliable, and relevant discovery of such resources a significant challenge. This challenge is especially pertinent for online databases, whose dynamic content is largely opaque to contemporary search engines. The Neuroscience Information Framework
The Neuroscience Information Framework (NIF), http://neuinfo.org
The wide-scale development of ontologies in the bioinformatics domain facilitates their use in the creation of scientific workflows. To speed up the design of workflows, a Service Suggestion Engine is interfaced to the Galaxy Tool Integration and Workflow Platform. This enables users to ask for suggestions (e.g., what operation should go next) while designing workflows with the Galaxy user interface. The Service Suggest Engine utilizes semantic annotations to suggest appropriate Web service operations to plug into the workflow under design. The enriched Ontology for Biomedical Investigation (OBI) is used as a target for the annotations. The effectiveness of the suggestions provided is evaluated against a consensus of domain experts.
Voids are extremely important to water science, because their size and connectivity determines the storage and flow of water both above and below the ground surface. While previous formal theories about voids strictly consider holes hosted inside objects, we generalize voids to also include spaces between objects, and distinguish voids in macroscopic objects from those occurring microscopically in an object's matter. These notions are axiomatized in first-order logic as an extension of the DOLCE ontology, and are applied to key aspects of hydrology and hydrogeology, laying the groundwork for a foundational hydro ontology.
Moving from some reflections on the empirical practice of measurement and on the nature of visual perception, we present a constructivist approach to objects. At the basis of such approach there is the idea that all we may know about what is out there is always mediated by some sort of apparatus, being it a measurement instrument or our perceptual system. Given this perspective, some questions are in order: how are objects identified and re-identified through time from the outcomes of apparatuses? How can we distinguish different (kinds of) objects? Our first goal will be to make explicit the mechanism used to build objects from the apparatuses' outcomes, emphasizing what are the ontological and representational problems this construction faces. A second contribution will be a preliminary discussion of some possible ways to distinguish social objects, the constructed objects par excellence, from physical ones. A third contribution will be an attempt to make a bridge between two scientific communities that rarely seek contact or mutual recognition: that of formal ontologies and that of formal concept analysis.
Recently, the demand for data integration on the Geological domain has increased. Most approaches for database schema integration are strongly based on structure and syntax, and present limitations. Semantic resources, such as ontologies, have been used to reach better results for data integration. However, these approaches assume there are already local ontologies that represent the databases involved in the interoperation. Furthermore, the creation of an ontology based on the database logical schema is not an easy task. On the other hand, it had been proposed that the association of a top-level ontology to a database conceptual schema may lead to better interoperability results. The idea is to make explicit the ontological commitment of each representation, and thus facilitate their integration. This work presents a case study on the Geological domain, which aimed at making explicit the ontological commitment of a database conceptual schema, in order to further improve data interoperability. The main contribution of this work is that it covers the whole process. It starts from the database logical schema, applies a set of reverse engineering techniques to create a preliminary database conceptual schema, and then uses a top-level ontology as a way of making explicit its ontological commitment. A detailed description is provided on how each step was taken, serving as a roadmap for others that may need to go through a similar process on the geological domain or on other domains.
To stay competitive within the market, organizations need to understand the skills and competencies of their human resources in order to best utilize them. This paper focuses on the problem of modeling human resources in a dynamic environment, and presents a formal ontology for representing, inferring, and validating skills and competencies over time.
Both natural objects and artifacts have been studied from a variety of perspectives by the different sciences. One issue that has so far resisted philosophical and ontological investigations is the definition of a general notion of function capable of making sense of the functions attributed to natural objects, such as biological organisms, as well as of the functions attributed to artifacts, such as (designed) tools.
The paper starts from the notions of role and context to study a definition already used to define artifact functions. The clarification of types of functional contexts and of the role of intentionality in defining function leads to a new proposal that applies to functions of natural objects as well as of artifacts. Finally, we evaluate our proposal against some desiderata discussed in the literature.
The aim of this paper is to offer a conceptual analysis of the notion of failure of engineering artifacts focusing on aspects that are of import for a possible ontological formalization. Failure is a central notion in engineering, yet different taxonomies exist in the various industries and engineering domains that are not mutually compatible thereby hindering knowledge exchange. A formal definition of failure would contribute to improve knowledge exchange. However, in order to be successful such formalization should rest on shared conceptualizations. The paper analyses how the notion of failure is used in engineering, starting with the so-called “traditional definition”. Then, it is shown that engineers are willing to consider as failures also events and circumstances that are at odds with this traditional definition. Therefore, it is argued that, in order to capture adequately engineering conceptualizations, three independent notions of failure should be distinguished, which are called function-based failure, specification-based failure, and material-based failure.
The construction of complex ontologies can be facilitated by adapting existing vocabularies. There is little clarity and in fact little consensus as to what modifications of vocabularies are necessary in order to re-engineer them into ontologies. In this paper we present a method that provides clear steps to follow when re-engineering a thesaurus. The method makes use of top-level ontologies and was derived from the structural differences between thesauri and ontologies as well as from best practices in modeling, some of which have been advocated in the biomedical domain. We illustrate each step of our method with examples from a re-engineering case study about agricultural fertilizers based on the AGROVOC thesaurus. Our method makes clear that re-engineering thesauri requires far more than just a syntactic conversion into a formal language or other easily automatable steps. The method can not only be used for re-engineering thesauri, but does also summarize steps for building ontologies in general, and can hence be adapted for the re-engineering of other types of vocabularies or terminologies.
In the field of software engineering component-based development and appropriate documentation are established methods to support reuse. While modular development is tackled in various work regarding ontology engineering, it is an open problem how documentation of ontologies should be created. After analyzing existing ontology documentations we identified grouping concepts as a very helpful technique to simplify the understandability and thus improve the reusability of ontologies. In this paper, we present a technique to group concepts for ontology documentation by applying community detection algorithms on the graph structure of ontologies. Using the manually created concept groups from existing documentations as reference we demonstrate that this technique is able to create appropriate concept groups automatically.
The complexity of ontology authoring and the difficulty to master the use of existing ontology authoring tools, put significant constraints on the involvement of both domain experts and knowledge engineers in ontology authoring. This often requires substantial effort for fixing ontologies defects (e.g. inconsistency, unsatisfiability, missing or unintended implications, redundancy, isolated entities). The paper argues that ontology authoring tools should provide immediate semantic feedback upon entering ontological constructs. We present a framework to analyse input axioms and provide meaningful feedback at a semantic level. The framework has been used to augment an existing Controlled Natural Language-based ontology authoring tool – ROO. An experimental study with ROO has been conducted to examine users' reactions to the semantic feedback and the effect on their ontology authoring behaviour. The study strongly supported responsive intuitive ontology authoring tools, and identified future directions to extend and integrate semantic feedback.
The paper defines three logical criteria for semantic adequacy of an applied ontology. All criteria are based on the idea to the effect that when an ontology construed as a formal theory allows for swapping some items in its vocabulary, then it does not sufficiently differentiate between the meanings of these items and, consequently, the semantic aspect of this vocabulary cannot be claimed to be sufficiently characterised. Besides providing the formal definitions of those criteria and proving some simple correlations therebetween I present the empirical results of their implementation.
In this paper we review the integration of BFO's theory of types with OntoClean's notion of Rigidity, provide our decision tree procedure for evaluating ontologies based on the integration, while also describing its implementation as a Protégé 4 plugin, the BFO-Rigidity Decision Tree Wizard. Finally we provide a practical analysis of controversial and important ontological topics surrounding the BFO-Rigidity integration work. The decision tree approach allows our wizard plugin to implicitly perform inferences on behalf of a modeler based on answers to questions. This approach is accessible because it does not require familiarity with BFO, OntoClean, or our first-order formal system, and does not require the modeler to make assertions that are not normally considered within the scope of a domain level ontology. Having chosen for our implementation a plugin environment that interoperates with a popular ontology editor, we expect that the principles underlying the integration work will become more accessible to both novice and expert domain modelers.
This paper provides a reformulation of OntoClean's notion of Unity and Identity within a formal theory of classes, and evaluates how the reformulations apply to BFO's theory of types, which was previously given within the same formal theory. For Unity, a definition schema and explication together express the underlying dependency between a unifying relation and some proper subrelation of the ‘part of’ relation, which together define how a particular of a class is a whole. For Identity, the notion of an identity criterion is ontologically grounded and formalized as an identity procedure. For both Unity and Identity the formulations are expressed within a sorted first-order logic, where staying within first-order expressivity proved difficult in past work. With our reformulations in hand we evaluate the primary type dichotomy for material entities of BFO, Object and ObjectAggregate. Together with the work that integrates OntoClean's notion of Rigidity with BFO's theory of types, this work augments ongoing efforts to build software designed to evaluate and standardize OBO Foundry candidate ontologies, of which BFO is the upper level ontology.
We describe our effort in defining change-of-state words from Core WordNet by constructing axioms anchored in core theories that are crucial in characterizing event words, including change of state, composite entity, scales and event structure. Our methodology consists of three steps: Analyzing the structure of a word's WordNet senses, writing axioms for the most general senses, and testing the axioms on textual entailment pairs. We also describe some common issues we faced and decisions we had to make during axiomatization. We look at two specific textual entailment examples in detail to illustrate the power of this method.
In this paper, we propose to put together the intuition developed in the descriptive work by Cusic on plurality in the verbal domain and the formal tools developed by Landman on groups. Cusic's hierarchy is used to say something both on the accessibility of the members of a plurality, and on the iteration of pluralisation to produce predefined new units. The notion of structured unit such as a group introduces a breaking point in the transitive relation that is part of the definition of the partial order imposed on the denotation of a predicate. Looking inside a group means to jump out of the semilattice to which the group belongs, and to land into another semilattice generated by a set of elements that are units (or collections thereof) of a different layer and are associated with a different sub-sortal. Discourse accessibility of the elements in the landing structure is not warranted.
We are developing an ontology of microsocial concepts for use in an instructional system for teaching cross-cultural communication. We report here on that part of the ontology relating to interpersonal relationships. We first explicate the key concepts of commitment, shared plans, and good will. Then in terms of these we present a formal account of simple exchanges, the host-guest relationship, and friendship.
