Formal Rigor Research Articles

Evaluation of the Cell Ontology (CL)

AbstractAn ontological representation of the entities relevant to biological research is urgently needed. The cell ontology developed by Bard and colleagues (CL) (Bard et al. 2005) makes a significant contribution towards fulfilling this need by providing an ontology of cell types. The CL has already proven useful for data annotation (e.g. Grumbling et al. 2006), although the ontology’s potential utility goes well beyond that specific application. For example, using the number of distinct cell types in an organism as a measure of biological complexity, Vogel and Chothia (2006) compared the proteomes of 38 organisms of varying complexity and identified patterns in the evolution and expansion of protein domain superfamilies. This work has implications for some of the fundamental questions in biology, such as understanding the processes by which physiology becomes more intricate, new cell types arise, and biological complexity increases. While Vogel and Chothia did not yet utilize the CL for this work, they cite Bard et al. (2005) and describe the ontology’s value for improving and extending their analysis. Thus, in addition to its great utility for database annotation, the CL has the potential to play a significant role in basic scientific inquiry.The prospect of using the CL (and other ontologies) for this type of scientific research is extremely exciting but also imposes requirements on the level of formal rigor applied in ontology development, on the adequacy of the ontology as a representation of reality, and on its adherence to community standards of best practice. It is with these things in mind that I examined the CL to determine whether any revision would be required before my research group could use it for scientific research.After carefully evaluating the CL, my overall impression is that it does not possess the rigor and exactness required of a reference ontology. Furthermore, the problems I see are significant enough that it would be difficult for my research group to use the CL as our application ontology. While some of the problems could be resolved by changing a relation or rewriting a definition, others would require careful rethinking of the ontology’s foundation, because they involve the scope and organizing principle of the ontology as a whole.

Motion Generation in the MRROC++ Robot Programming Framework

In this paper we present a formal approach to robot motion specification. This motion specification takes into account three elementary behaviors that suffice to define any robot interaction with the environment, i.e. free motion, exerting generalized forces and the transition between both of these behaviors. These behaviors provide a foundation for general motion generation taking into account any sensors, any effectors and the capability to exchange information between embodied agents. This specification can be used both for the definition of robot tasks and implementation of robot control software, hence both of those aspects are presented in this paper. This formal approach was used for the implementation of the MRROC++ robot programming framework. Two-handed manipulation of a Rubik’s cube is used as an exemplary task. Extensive experimentation both with the presented formalism and the MRROC++ framework showed that the imposed formal rigor eliminates many errors at the software specification phase, produces well-structured control software and significantly speeds up and simplifies its implementation. These advantages are mainly due to the fact that the proposed formal specification tool is derived from operational semantics used in computer science for the definition of programming languages, thus a close relationship between abstract definition and the implementation of the control system resulted.

An improved ontological representation of dendritic cells as a paradigm for all cell types.

BackgroundRecent increases in the volume and diversity of life science data and information and an increasing emphasis on data sharing and interoperability have resulted in the creation of a large number of biological ontologies, including the Cell Ontology (CL), designed to provide a standardized representation of cell types for data annotation. Ontologies have been shown to have significant benefits for computational analyses of large data sets and for automated reasoning applications, leading to organized attempts to improve the structure and formal rigor of ontologies to better support computation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL's utility for computation and for cross-species data integration.ResultsTo enhance the CL's utility for computational analyses, we developed a method for the ontological representation of cells and applied this method to develop a dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. We avoid multiple uses of is_a by linking DC-CL terms to terms in other ontologies via additional, formally defined relations such as has_function.ConclusionThis approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. Accordingly, we propose our method as a general strategy for the ontological representation of cells. DC-CL is available from .

Voice-supported Electronic Health Record for Temporomandibular Joint Disorders

Objective: Biomedical ontologies exist to serve integration of clinical and experimental data, and it is critical to their success that they be put to widespread use in the annotation of data. How, then, can ontologies achieve the sort of user- friendliness, reliability, cost-effectiveness, and breadth of coverage that is necessary to ensure extensive usage? Methods: Our focus here is on two different sets of answers to these questions that have been proposed, on the one hand in medicine, by the SNOMED CT community, and on the other hand in biology, by the OBO Foundry. We address more specifically the issue as to how adherence to certain development principles can advance the usability and effectiveness of an ontology or terminology resource, for example by allowing more accurate maintenance, more reliable application, and more efficient interoperation with other ontologies and information resources. Results: SNOMED CT and the OBO Foundry differ considerably in their general approach. Nevertheless, a general trend towards more formal rigor and cross-domain interoperability can be seen in both and we argue that this trend should be accepted by all similar initiatives in the future. Conclusions: Future efforts in ontology development have t o address t he need f or harmonization and integration of ontologies across disciplinary borders, and for this, coherent formalization of ontologies is a pre-requisite.

Putting Biomedical Ontologies to Work

Objectives Biomedical ontologies exist to serve integration of clinical and expe- rimental data, and it is critical to their success that they be put to widespread use in the annotation of data. How, then, can ontologies achieve the sort of user- friendliness, reliability, cost-effectiveness, and breadth of coverage that is necessary to ensure extensive usage? Methods Our focus here is on two different sets of answers to these questions that have been proposed, on the one hand in medicine, by the SNOMED CT community, and on the other hand in biology, by the OBO Foundry. We address more specifically the issue as to how adherence to certain development principles can advance the usability and effectiveness of an ontology or terminology resource, for example by allowing more accurate maintenance, more reliable application, and more e f f i c i ent interoperation with other ontologies and information resources. Results SNOMED CT and the OBO Foundry differ considerably in their general approach. Nevertheless, a general trend towards more formal rigor and cross-domain interoperability can be seen in both and we argue that this trend should be accepted by all similar initiatives in the future. Conclusions Future efforts in ontology development have t o address t he need f or harmonization and integration of ontologies across disciplinary borders, and for this, coherent formalization of ontologies is a pre-requisite.

“Spirit of Place” as Process: Archaeography, Dowsing and Perceptual Mapping at Belas Knap

“Spirit of place,” or genius loci, is both an abstract concept and a profoundly personal experience of relationship with place. Each place and district and region has its own characteristics, both explicit and implicit, that make it “locally distinctive,” to use the term coined by the English charity Common Ground. As such, it provides a rich seam of interest for archaeography—archaeology's artistically-oriented cousin.Using examples from a long-term archaeography project at and around the Belas Knap long-barrow in south-west England, this paper explores an approach in which, by combining the formal rigor of archaeology with disciplines from a variety of other sources, “spirit of place” can be transformed from metaphor to method, yielding not only new insights about past and present, but also concrete archaeological evidence about habitation and use.

Poetyka a światopogląd. O twórczości Marii Pawlikowskiej-lasnorzewskiej

Part ONE. This dissertation is devoted to the inspiration of Maria Pawlikowska-Jasnorzewska by the philosophy of the East, which she got to know through Arthur Schopenhauer's writings. The first part contains a description of the manner in which the poet interpreted the inconsistency of the conception of the German philosopher who tried to combine in one all the elements of various religious and philosophical trends coming from India. We can look on Maria Pawlikowska-Jasnorzewska's works of the pre-World War II years as on a peculiar literary adaptation of these various ideas, and, to be more exact, as on an attempt to construct such a poetic world in which there might be a coordination between diverse currents determined by the Brahminian and the Buddhist ideas. In Pawlikowska-Jasnorzewska's early poems affirmation, paradox, (self/auto)irony and degradation of loftiness are concurrent, which are characteristic of the Buddhist attitude to the world and there is also avoidance of reflection of ethical nature so characteristic of Brahminism.Part two. In the second part of the dissertation on the influence of Indian philosophy on Maria Pawlikowska-Jasnorzewska's views, these elements of her writings are analysed (such as miniaturisation, condensation, formal rigour, intellectualisation of lyricism), which reflected her way of thinking. The description also contains the next stage of writing activity of the author of Krystalizacje [Crystallisations] during which the poet gave up the affirmative amoralism, and in her poetry occurred a confrontation of the negativist assumptions of Brahminism with the Buddhist imperative of mercy. Along with the acceptance of the evaluative perspective in Pawlikowska-Jasnorzewska's poetic diction elements of gnostic rhetoric began to appear in which she followed Schopenhauer, and in her writings the process of "decay of the poetic form" began to be more and more visible, which was described by critics, and which led through the poetics of a sketch and fragment in her later prewar works to the notebook-like last recordings of the war period.

Indian Modernity and Tagore's Dance

Rabindranath Tagore's invention of an entirely new dance style liberated dance from the formulaic choreography and narratives of classical Indian dance. Tagore advocated naturalistic rather than stylized expression, with the stated purpose of creating an aesthetic vehicle for conveying the drama of human emotional experience. This style, Rabindra-nritya, the first ‘modern dance’ of India, was and has remained entirely uncodified, relying on the creative impulse of the individual dancer interpreting poetical compositions. This flexibility, however, has tended to be accompanied by a lack of formal rigour and codification, which may help explain why Rabindranath's dance style has never gained acceptance in India as a serious art beyond the Bengali cultural domain.

Indian Modernity and Tagore's Dance

Abstract Rabindranath Tagore's invention of an entirely new dance style liberated dance from the formulaic choreography and narratives of classical Indian dance. Tagore advocated naturalistic rather than stylized expression, with the stated purpose of creating an aesthetic vehicle for conveying the drama of human emotional experience. This style, Rabindra-nritya, the first ‘modern dance’ of India, was and has remained entirely uncodified, relying on the creative impulse of the individual dancer interpreting poetical compositions. This flexibility, however, has tended to be accompanied by a lack of formal rigour and codification, which may help explain why Rabindranath's dance style has never gained acceptance in India as a serious art beyond the Bengali cultural domain.

Lygia Pape

Lygia Pape’s career is entwined with the history of Brazilian art in the second half of the twentieth century. Her work and artistic position, which brought together formal rigour and daring experi...

Propositional Statecharts for Agent Interaction Protocols

Current representations of interaction protocols either concentrate on ease of understanding and neglect the need to specify protocols unambiguously (e.g. [B. Bauer, J.P. Muller, J.Odell, Agent UML: A Formalism for Specifying Multiagent Software Systems, AOSE (2000) 91–104]), or concentrate on formal rigour and neglect usability issues (e.g. [S. Paurobally, Rational Agents and the Processes and States of Negotiation, Ph.D. thesis, Imperial College, London, 2002, N. Fornara, M. Colombetti, Defining Interaction Protocols using a Commitment Based Agent Communication Language, Proceedings of the Second International Joint Conference on Autonomous Agents and Multiagent Systems (2003)]). The on-going development of propositional statecharts has been motivated by the need to provide a notation which satisfies both of these requirements. Here we give a brief description of propositional statecharts, a restricted form of David Harel's state-chart formalism [D. Harel, Statecharts: A visual formalism for complex systems, Sci. Comput. Programming 8 (1987) 231–274] designed to represent agent interaction protocols. Statecharts are a popular extension of Euler Diagrams and are widely used as part of the UML framework. Propositional statecharts take advantage of the intuitive nature of the statechart formalism, and include labelling conventions to ensure that interaction protocols are defined unambiguously while remaining easy to understand.

A Pasinettian approach to international economic relations: the pure labor case

In this paper, the pure labor version of Pasinetti's model of structural change and economic dynamics is extended to consider international economic relations. The conditions for full employment, full expenditure of national income and trade balance equilibrium are established along with solutions for the systems of physical quantities and prices in an open economy. Analytical results concerning the benefits of international trade and learning are studied with formal rigor. Then static and dynamic aspects of the principle of comparative cost advantages are analyzed considering the determinants of the level of specialization and international prices.

The music of Luigi Dallapiccola

Luigi Dallapiccola (1904-1975) was one of the most important Italian composers of the twentieth century. As well as writing several operas, he composed a large number of works in which the human voice, whether in solo or in chorus, plays an important role. Dallapiccola also set texts by writers as diverse as James Joyce, Salvatore Quasimodo, Antonio Machado, Goethe, and Heine. This book is the first in English to deal with Dallapiccola as a whole, from the first, hesitant vocal compositions of his student years up to the works of his last decade, in which Italian lyricism is combined with great formal rigor. The author suggests that Dallapiccola should be understood not only as an influential figure in the post-war developments of Italian music, but also as one who renewed and revitalized the older traditions of Italian music. Raymond Fearn is Professor of Music, Keele University.

Teaching electromagnetic waves to electrical engineering students: an abridged approach

This paper describes the rationale of a one semester sophomore level basic course on electromagnetic waves for electrical engineers (emphasis on communications), which avoids the mathematical complexity associated with Maxwell's equations (differential operators, vector potential, wave equation) with no loss of logical rigor nor substantial loss of formal rigor. The course is based in the postulation of the fields produced by an accelerated charge in the nonrelativistic limit, and the obtainment of a uniform plane wave as the limiting case of a spherical wave when observed far from the source. In this way, the student can begin working with the full vector description of electromagnetic waves and with relevant scientific and technical examples from the second course week, and his/her effort is directed more to the use and interpretation of waves than to their mathematical derivation. Further postulation of the Huygens-Fresnel principle puts the student in a position to tackle most of the basic problems of wave optics and radiation systems. Although some penalties are paid by this approach (more additional postulates are required; students miss the ability to solve boundary value problems; engineering textbooks are not written with this background; professors feel attached to the classical approach), it has been found much more efficient than the standard Maxwell's equations as an introduction to telecommunication topics. Also, students find it more interesting, motivating, and rewarding.

Historical evolution and mathematical models: A sociocultural algorithm

Though there are a lot of approaches to the problem of sociocultural evolution most of them are only one-sided, i.e., they deal only with either social or cultural processes. With few exceptions they are also only informal theories with no formal rigour. In this article we propose a theoretical model which considers both sides of the problem, that is the mutual interdependence of the evolution of social structures and of the culture of a society. A mathematical model, the sociocultural algorithm (SCA), based on these theoretical considerations maps several of the dynamic characteristics of sociocultural evolution, suggesting that universal principles underlie the dynamics of historical evolution.

Some Ontological Remarks about Music Composition Processes

However, the role of algorithms (finite computable functions, in Turing's sense) is not to be simply reified in a composition. Composers use computers not only as numbercrunching devices, but also as interactive partners to perform operations where the output depends on actual performance. Composers are concerned with the creation of musical situations emerging concretely of a critical interaction with their materials, including their algorithms. This task cannot be exhausted by a linear (a priori, non-interactive) problem-solving approach. Interaction is here matching an important feature of musical composition processes, giving room for the emergence of irreducible situations through non-linear interaction. Irreducibility is perhaps a key word in this context, as we are dealing with music's categories and ends. Music is not dependent on logical constructs unverified by physical experience. Composers, especially those using computers, have learned-sometimes painfully-that the formal rigor of a generative function does not guarantee by itself the musical coherence of a result. Music cannot be confused with (or reduced to) a formalized discipline: even if music actually uses knowledge and tools coming from formalized disciplines, formalization does not play a foundational role in regard to musical processes. I will refer in this article to a realist ontological principle relying on commitment to action which can shed light on the nature of musical compositional processes in regard to formal constructivism. Additionally, musical processes, at least from the composer's point of view, are not situations out there waiting to be discovered: they are rather to be composed (since they did not exist anywhere before being composed), and hence they cannot be considered properly as modeling activities, even if they use-and deeply absorb-models, knowledge, and tools coming from scientific domains (acoustic and psychoacoustic modeling, for example). In fact, music transforms this knowledge and these tools into its own ontological concern: to create specific musical situations (musical states of affairs). To this end, a palette of diverse compositional instances is needed, including strategies for controlling and qualifying results and choices, according to a given musical project. These compositional instances, to reiterate, are not envisaged here in the frame of the traditional approach to algorithmic (automatic) composition: they are instead seen in the light of the ongoing paradigm shift from algorithmics to interaction (Wegner 1997, Bello 1997), where the general-purpose computer is regarded as one component of complex systems (Winograd 1979), and where the composer, being another component of these complex systems, is imbedded in a network within which he or she can act, design, and experience concrete tools and (meaningful) musical situations. It is under this perspective, I believe, that the formal status of musical processes can be approachedin a certain way revisited-as I will try to do in this article, focusing on ontological questions. Computer music practice (computer-generated and computer-assisted composition) is of course the underlying frame of the discussion here offered, because these reflections have arisen from the

Practical development of re-usable terminologies: GALEN-IN-USE and the GALEN Organisation

Medical terminology is now playing a key role in medical software. This requires new techniques with which many clinical users, classification experts and applications developers are unfamiliar. There is a conflict in that the more re-usable techniques for terminology needed to support sharing of information among many different applications are more difficult to use for any one application. A layered approach to re-use is described which combines techniques from first generation systems and relatively easily understood second generation systems with the formal rigour of third generation systems to resolve this conflict. The methodology also provides a potentially rigorous approach to defining the relationship between terminology and structure in the electronic healthcare record architecture. It provides a natural migration pathway from existing systems to powerful re-usable multilingual terminologies.

Formalizing Database Recovery

Failure resilience is an essential requirement for database systems, yet there has been little e ort to specify and verify techniques for failure recovery formally. The desire to improve performance has resulted in algorithms of considerable sophistication, yet understood by few and prone to errors. In this paper, we illustrate how the methodology of Gurevich Abstract State Machines can elucidate recovery and provide formal rigor to the design of a recovery algorithm. In a series of re nements, we model a recovery algorithm at several levels of abstraction, verifying the correctness of each model. This work suggests that our approach can be applied to more advanced recovery mechanisms.

What Are Infinitesimals and Why They Cannot Be Seen

Visualizing mathematical structures is a broad and important subject in mathemat- ics education. Consider, for example, the difficulty of seeing a number system that includes infinitesimals. This might seem an obvious observation since infinitesimals are infinitely small, but that is not the point I wish to make here. In mathematics we have tools that allow us to think visually about objects far beyond direct physical perception. We can see the infinite. We use our natural intuition of the geometiy of three dimensional space as a starting point for constructions of abstract mathematical structures, such as higher dimensional vector spaces, non- euclidean geometries, and topological spaces of various kinds. Those structures often do not seem to have direct interpretations in the physical universe we know, but nevertheless we can picture them in the mind's eye. With simple images we can illustrate, quite accurately, more abstract concepts. Precision and formal rigor are essential in mathematics, but these qualities apply only to the final products of mathematical activity. When we domathemat- ics, we rarely think formally. We do not limit ourselves to computations and rigorous proofs. Rather, mathematicians work with pictures visual representa- tions of mathematical structures. The same pictures also seem indispensable in learning mathematics. Some mathematical structures, however, cannot be visual- ized easily. A level of abstraction and set theoretic methods are necessary to prove that certain structures even exist. A theorem of Stanley Tennenbaum's (5), pub- lished in 1959, states that certain mathematical structures are very complex. The notion of complexitz7, as used in Tennenbaum's theorem, has precise meaning, and I will say more about it later. At this point let me just mention that the theorem excludes the possibility of a simple presentation of some structures, and the number system of nonstandard analysis is one of them. Nonstandard analysis was created (or perhaps recreated) by Abraham Robinson (4), who reintroduced infinitesimals to mathematics using the formal apparatus of mathematical logic. Since then, much has been written on the theory of infinitesi- mals and their applications. Part of the effort was directed towards utilizing some of the new methods and techniques in teaching. Nonstandard analysis offers great simplicity in defining basic concepts. Think, for example, of the following defini- tion of the derivative: y = f(x) is differentiable at a point a, and b is the derivative of f(x) at a, if for every number dx infinitesimally close to 0, dy ff a + dsc) - f( a)

Virtual mathematics

The single biggest problem we face is that of visualisationRichard P. Feynman, Los Alamos 1945Given the critical dependence of our civilisation on mathematics, it is paradoxical that it lacks any general acclaim or popularity, and usually invokes fear and mysticism. Perhaps this is because, for most of us, the process of acquiring mathematical skills is somewhat protracted and painful. It is often perceived as a nightmare topic, which engenders a defence mechanism of open ignorance that is often lauded. In truth, most people can become reasonably competent. However, the time and effort needed to acquire the formal rigour for even a modest capability is often seen as excessive by modern standards.