Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature.

BACKGROUND: The wealth of phenotypic descriptions documented in the published articles, monographs, and dissertations of phylogenetic systematics is traditionally reported in a free-text format, and it is therefore largely inaccessible for linkage to biological databases for genetics, development, and phenotypes, and difficult to manage for large-scale integrative work. The Phenoscape project aims to represent these complex and detailed descriptions with rich and formal semantics that are amenable to computation and integration with phenotype data from other fields of biology. This entails reconceptualizing the traditional free-text characters into the computable Entity-Quality (EQ) formalism using ontologies. METHODOLOGY/PRINCIPAL FINDINGS: We used ontologies and the EQ formalism to curate a collection of 47 phylogenetic studies on ostariophysan fishes (including catfishes, characins, minnows, knifefishes) and their relatives with the goal of integrating these complex phenotype descriptions with information from an existing model organism database (zebrafish, http://zfin.org). We developed a curation workflow for the collection of character, taxonomic and specimen data from these publications. A total of 4,617 phenotypic characters (10,512 states) for 3,449 taxa, primarily species, were curated into EQ formalism (for a total of 12,861 EQ statements) using anatomical and taxonomic terms from teleost-specific ontologies (Teleost Anatomy Ontology and Teleost Taxonomy Ontology) in combination with terms from a quality ontology (Phenotype and Trait Ontology). Standards and guidelines for consistently and accurately representing phenotypes were developed in response to the challenges that were evident from two annotation experiments and from feedback from curators. CONCLUSIONS/SIGNIFICANCE: The challenges we encountered and many of the curation standards and methods for improving consistency that we developed are generally applicable to any effort to represent phenotypes using ontologies. This is because an ontological representation of the detailed variations in phenotype, whether between mutant or wildtype, among individual humans, or across the diversity of species, requires a process by which a precise combination of terms from domain ontologies are selected and organized according to logical relations. The efficiencies that we have developed in this process will be useful for any attempt to annotate complex phenotypic descriptions using ontologies. We also discuss some ramifications of EQ representation for the domain of systematics.

15N NMR relaxation data reveal significant chemical exchange broadening in the alpha-domain of human α-lactalbumin

Human alpha-lactalbumin (alpha-LA), a 123-residue calcium-binding protein, has been studied using (15)N NMR relaxation methods in order to characterize backbone dynamics of the native state at the level of individual residues. Relaxation data were collected at three magnetic field strengths and analyzed using the model-free formalism of Lipari and Szabo. The order parameters derived from this analysis are generally high, indicating a rigid backbone. A total of 46 residues required an exchange contribution to T(2); 43 of these residues are located in the alpha-domain of the protein. The largest exchange contributions are observed in the A-, B-, D-, and C-terminal 3(10)-helices of the alpha-domain; these residues have been shown previously to form a highly stable core in the alpha-LA molten globule. The observed exchange broadening, along with previous hydrogen/deuterium amide exchange data, suggests that this part of the alpha-domain may undergo a local structural transition between the well-ordered native structure and a less-ordered molten-globule-like structure.

Consistent couplings between fields with a gauge freedom and deformations of the master equation

The antibracket in the antifield-BRST formalism is known to define a map Hp × Hq → Hp + q + 1 associating with two equivalence classes of BRST invariant observables of respective ghost number p and q an equivalence class of BRST invariant observables of ghost number p + q + 1. It is shown that this map is trivial in the space of all functionals, i.e. that its image contains only the zeroth class. However, it is generically non-trivial in the space of local functionals. Implications of this result for the problem of consistent interactions among fields with a gauge freedom are then drawn. It is shown that the obstructions to constructing non-trivial such interactions lie precisely in the image of the antibracket map and are accordingly non-existent if one does not insist on locality. However consistent local interactions are severely constrained. The example of the Chern-Simons theory is considered. It is proved that the only consistent, local, Lorentz covariant interactions for the abelian models are exhausted by the non-abelian Chern-Simons extensions. © 1993.

Temporal structure and enablement representation for mutual wills: A Petri net approach

Those temporal formalisms that are sporadically found nowadays in the literature of AI & Law are based on temporal logic. We claim a revived role for another major class of temporal representation: Petri nets. This formalism, popular in computing from the 1970s, had its potential recognized on occasion in the literature of legal computing as well, but apparently the discipline has lost sight of it, and its practitioners on average need be tutored into this kind of representation. Asynchronous, concurrent processes—for which the approach is well‐suited—are found in the legal domain, in disparate contexts. We develop an example for Mutual Wills.

Representing temporal knowledge in legal discourse

This paper presents a formalism for representing temporal knowledge in legal discourse that allows an explicit expression of time and event occurrences. The fundamental time structure is characterized as a well‐ordered discrete set of primitive times, i.e. non‐decomposable intervals with positive duration or points with zero duration), from which decomposable intervals can be constructed. The formalism supports a full representation of both absolute and relative temporal knowledge, and a formal mechanism for checking the temporal consistency of a given set of legal statements is provided. The general consistency checking algorithm which addresses both absolute and relative temporal knowledge turns out to be a linear programming problem, while in the special case where only relative temporal relations are involved, it becomes a simple question of searching for cycles in the graphical representation of the corresponding legal text.

Guest Editorial. Special Issue: Temporal logic in engineering

Logic-based models are thriving within artificial intelligence. A great number of new logics have been defined, and their theory investigated. Epistemic logics introduce modal operators for knowledge or belief; deontic logics are about norms, and introduce operators of deontic necessity and possibility (i.e., obligation or prohibition). And then we have a much investigated class—temporal logics—to whose application to engineering this special issue is devoted. This kind of formalism deserves increased widespread recognition and application in engineering, a domain where other kinds of temporal models (e.g., Petri nets) are by now a fairly standard part of the modelling toolbox.

Representing temporal relationships between events and their effects

Temporal relationships between events and their effects are complex. As the effects of a given event, a proposition may change its truth value immediately after the occurrence of the event and remain true until some other events occur, while another proposition may only become true/false from some time after the causal event has occurred. Expressing delayed effects of events has been a problematic question in most existing theories of action and change. This paper presents a new formalism for representing general temporal causal relationships between events and their effects. It allows expressions of both immediate and delayed effects of events, and supports common-sense assertions such as "effects cannot precede their causes".

On the coupling of Navier–Stokes and linearised Euler equations for aeroacoustic simulation

Aerodynamic generation of sound is governed by the Navier–Stokes equations while acoustic propagation in a non-uniform medium is effectively described by the linearised Euler equations. Different numerical schemes are required for the efficient solution of these two sets of equations, and therefore, coupling techniques become an essential issue. Two types of one-way coupling between the flow solver and the acoustic solver are discussed: (a) for aerodynamic sound generated at solid surfaces, and (b) in the free stream. Test results indicate how the coupling achieves the necessary accuracy so that Computational Fluid Dynamics codes can be used in aeroacoustic simulations.

Maintenance of a case-base for the retrieval of rotationally symmetric shapes for the design of metal castings

In this paper, we discuss the problem of maintenance of a CBR system for retrieval of rotationally symmetric shapes. The special feature of this system is that similarity is derived primarily from graph matching algorithms. The special problem of such a system is that it does not operate on search indices that may be derived from single cases and then used for visualisation and principle component analyses. Rather, the system is built on a similarity metric defined directly over pairs of cases. The problems of efficiency, consistency, redundancy, completeness and correctness are discussed for such a system. Performance measures for the CBR system are given, and the results for trials of the system are presented. The competence of the current case-base is discussed, with reference to a representation of cases as points in an n-dimensional feature space, and a Gramian visualisation. A refinement of the case base is performed as a result of the competence analysis and the performance of the case-base before and after refinement is compared.

The application of fire and evacuation simulation in ship design

Fire and evacuation models with features such as the ability to realistically simulate the spread of heat and smoke and the human response to fire as well as the capability to model human performance in heeled orientations linked to a virtual reality environment that produces realistic visualisation of the modelled scenarios are now available and can be used to aid the engineer in assessing ship design and procedures. This paper describes the maritimeEXODUS ship evacuation and the SMARTFIRE fire simulation model and provides an example application demonstrating the use of the models used in pperforming fire and evacuation analysis for a large passenger ship partially based on the requirements of MSC circular 1033.

A framework for historical case-based reasoning

This paper presents a framework for Historical Case-Based Reasoning (HCBR) which allows the expression of both relative and absolute temporal knowledge, representing case histories in the real world. The formalism is founded on a general temporal theory that accommodates both points and intervals as primitive time elements. A case history is formally defined as a collection of (time-independent) elemental cases, together with its corresponding temporal reference. Case history matching is two-fold, i.e., there are two similarity values need to be computed: the non-temporal similarity degree and the temporal similarity degree. On the one hand, based on elemental case matching, the non-temporal similarity degree between case histories is defined by means of computing the unions and intersections of the involved elemental cases. On the other hand, by means of the graphical presentation of temporal references, the temporal similarity degree in case history matching is transformed into conventional graph similarity measurement.

Issues in delivering multimedia content to mobile devices

The scalability of a computer system is its response to growth. It is also depended on its hardware, its operating system and the applications it is running. Most distributed systems technology today still depends on bus-based shared memory which do not scale well, and systems based on the grid or hypercube scheme requires significantly less connections than a full inter-connection that would exhibit a quadratic growth rate. The rapid convergence of mobile communication, digital broadcasting and network infrastructures calls for rich multimedia content that is adaptive and responsive to the needs of individuals, businesses and the public organisations. This paper will discuss the emergence of mobile Multimedia systems and provides an overview of the issues regarding design and delivery of multimedia content to mobile devices.

Visualizing a temporal consistency checker

The notion of time plays a vital and ubiquitous role of a common universal reference. In knowledge-based systems, temporal information is usually represented in terms of a collection of statements, together with the corresponding temporal reference. This paper introduces a visualized consistency checker for temporal reference. It allows expression of both absolute and relative temporal knowledge, and provides visual representation of temporal references in terms of directed and partially weighted graphs. Based on the temporal reference of a given scenario, the visualized checker can deliver a verdict to the user as to whether the scenario is temporally consistent or not, and provide the corresponding analysis / diagnosis.

A versatile characterization of causal relationships

This paper introduces a framework for representing versatile temporal relationships between events and their effects. The framework is based on a simple time model which characterizes each time element as a subset of the set of real numbers and allows expression of both absolute time values and relative temporal relations. The formalism presented here formally specifies the so-called most general temporal constraint (GTC), which guarantees the common-sense assertion that “the beginning of the effect cannot precede the beginning of the cause”. It is shown that there are in fact 8 possible causal relationships which satisfy GTC, including cases where, on the one hand, effects start simultaneously with, during, immediately after, or some time after their causes, and on the other hand, events end before, simultaneously with, or after their causes. The causal relationships characterized in this paper are versatile enough to subsume those representatives in the literature.

A sound and complete reified temporal logic

There are mainly two known approaches to the representation of temporal information in Computer Science: modal logic approaches (including tense logics and hybrid temporal logics) and predicate logic approaches (including temporal argument methods and reified temporal logics). On one hand, while tense logics, hybrid temporal logics and temporal argument methods enjoy formal theoretical foundations, their expressiveness has been criticised as not power enough for representing general temporal knowledge; on the other hand, although current reified temporal logics provide greater expressive power, most of them lack of complete and sound axiomatic theories. In this paper, we propose a new reified temporal logic with a clear syntax and semantics in terms of a sound and complete axiomatic formalism which retains all the expressive power of the approach of temporal reification.