On Composing Separated Concerns, Composability and Composition Anomalies

It is generally acknowledged that separation of concerns is a key requirement for effective software engineering: it helps in managing the complexity of software and supports the maintainability of a software system. Separation of concerns makes only sense if the realizations in software of these concerns can be composed together effectively into a working program. The ability to compose systems from independently developed components that can be adapted and extended easily is a long-standing goal in the software engineering discipline. However, both research and practice have shown that composability of software is far from trivial and fails repeatedly. Typically this occurs when components exhibit complex behavior, in particular when multiple concerns are involved in a single component. We believe that, to address the composability problems, we need a better understanding of the requirements involved in successful composition, and in addition define the situations where composition fails. To this aim, in this paper we introduce a number of requirements for designlevel composability and define a category of composition problems that are inherent for given composition models, which we term as composition anomalies

Six questions on the construction of ontologies in biomedicine

(Report assembled for the Workshop of the AMIA Working Group on Formal Biomedical Knowledge Representation in connection with AMIA Symposium, Washington DC, 2005.) Best practices in ontology building for biomedicine have been frequently discussed in recent years. However there is a range of seemingly disparate views represented by experts in the field. These views not only reflect the different uses to which ontologies are put, but also the experiences and disciplinary background of these experts themselves. We asked six questions related to biomedical ontologies to what we believe is a representative sample of ontologists in the biomedical field and came to a number conclusions which we believe can help provide an insight into the practical problems which ontology builders face today

Mapping Aspects to Components

This document defines a representation of aspects in the component model. Such a representation requires modeling the available (primitive) components, defining the composition mechanism, and representing aspects as enhancements of components

Efficient Discovery of Ontology Functional Dependencies

Poor data quality has become a pervasive issue due to the increasing complexity and size of modern datasets. Constraint based data cleaning techniques rely on integrity constraints as a benchmark to identify and correct errors. Data values that do not satisfy the given set of constraints are flagged as dirty, and data updates are made to re-align the data and the constraints. However, many errors often require user input to resolve due to domain expertise defining specific terminology and relationships. For example, in pharmaceuticals, 'Advil' \emph{is-a} brand name for 'ibuprofen' that can be captured in a pharmaceutical ontology. While functional dependencies (FDs) have traditionally been used in existing data cleaning solutions to model syntactic equivalence, they are not able to model broader relationships (e.g., is-a) defined by an ontology. In this paper, we take a first step towards extending the set of data quality constraints used in data cleaning by defining and discovering \emph{Ontology Functional Dependencies} (OFDs). We lay out theoretical and practical foundations for OFDs, including a set of sound and complete axioms, and a linear inference procedure. We then develop effective algorithms for discovering OFDs, and a set of optimizations that efficiently prune the search space. Our experimental evaluation using real data show the scalability and accuracy of our algorithms.Comment: 12 page

An Analysis of Composability and Composition Anomalies

The separation of concerns principle aims at decomposing a given design problem into concerns that are mapped to multiple independent software modules. The application of this principle eases the composition of the concerns and as such supports composability. Unfortunately, a clean separation (and composition of concerns) at the design level does not always imply the composability of the concerns at the implementation level. The composability might be reduced due to limitations of the implementation abstractions and composition mechanisms. The paper introduces the notion of composition anomaly to describe a general set of unexpected composition problems that arise when mapping design concerns to implementation concerns. To distinguish composition anomalies from other composition problems the requirements for composability at the design level is provided. The ideas are illustrated for a distributed newsgroup system

Class Hierarchy Complementation: Soundly Completing a Partial Type Graph

We present the problem of class hierarchy complementa- tion: given a partially known hierarchy of classes together with subtyping constraints (“A has to be a transitive sub- type of B”) complete the hierarchy so that it satisfies all con- straints. The problem has immediate practical application to the analysis of partial programs—e.g., it arises in the process of providing a sound handling of “phantom classes” in the Soot program analysis framework. We provide algorithms to solve the hierarchy complementation problem in the single inheritance and multiple inheritance settings. We also show that the problem in a language such as Java, with single in- heritance but multiple subtyping and distinguished class vs. interface types, can be decomposed into separate single- and multiple-subtyping instances. We implement our algorithms in a tool, JPhantom, which complements partial Java byte- code programs so that the result is guaranteed to satisfy the Java verifier requirements. JPhantom is highly scalable and runs in mere seconds even for large input applications and complex constraints (with a maximum of 14s for a 19MB binary)