Ontology

A Unified Ontology-Based Process Model for Software Maintenance and Comprehension

Abstract

In this paper, we present a formal process model to support the comprehension and maintenance of software systems. The model provides a formal ontological representation that supports the use of reasoning services across different knowledge resources. In the presented approach, we employ our Description Logic knowledge base to support the maintenance process management, as well as detailed analyses among resources, e.g., the traceability between various software artifacts. The resulting unified process model provides users with active guidance in selecting and utilizing these resources that are context-sensitive to a particular comprehension task. We illustrate both, the technical foundation based on our existing SOUND environment, as well as the general objectives and goals of our process model.

Keywords: Software maintenance, process modeling, ontological reasoning, software comprehension, traceability, text mining.

An Ontological Software Comprehension Process Model

Abstract

Comprehension is an essential part of software maintenance. Only software that is well understood can evolve in a controlled manner. In this paper, we present a formal process model to support the comprehension of software systems by using Ontology and Description Logic. This formal representation supports the use of reasoning services across different knowledge resources and therefore, enables us to provide users with guidance during the comprehension process that is context sensitive to their particular comprehension task.

Keywords: Software maintenance, program comprehension, process modeling, ontological reasoning

An Ontology-based Approach for the Recovery of Traceability Links

Abstract

Traceability links provide support for software engineers in understanding the relations and dependencies among software artifacts created during the software development process. In this research, we focus on re-establishing traceability links between existing source code and documentation to support reverse engineering. We present a novel approach that addresses this issue by creating formal ontological representations for both the documentation and source code artifacts.

Ontology-based Program Comprehension Tool Supporting Website Architectural Evolution

Abstract

A challenge of existing program comprehension approaches is to provide consistent and flexible representations for software systems. Maintainers have to match their mental models with the different representations these tools provide. In this paper, we present a novel approach that addresses this issue by providing a consistent ontological representation for both source code and documentation. The ontological representation unifies information from various sources, and therefore reduces the maintainers’ comprehension efforts. In addition, representing software artifacts in a formal ontology enables maintainers to formulate hypotheses about various properties of software systems. These hypotheses can be validated through an iterative exploration of information derived by our ontology inference engine. The implementation of our approach is presented in detail, and a case study is provided to demonstrate the applicability of our approach during the architectural evolution of a website content management system.

Keywords: Program Comprehension, Software Evolution, Ontology, Automated Reasoning

Empowering the Enzyme Biotechnologist with Ontologies

Introduction

The FungalWeb Ontology is a knowledge representation vehicle designed to integrate information relevant to industrial applications of enzymes. The ontology integrates information from established sources and supports complex queries to the instantiated FungalWeb knowledge base. The ontology represents prototype Semantic Web technology customized to the domain of industrial enzymes with a focus on enzyme discovery, commercial enzyme products and vendors, and the industrial applications and benefits of industrial enzymes. Using a series of application scenarios we demonstrate the utility of this 'Semantic Web' infrastructure to the enzyme biotechnologist.

Ontology Design for Biomedical Text Mining

Abstract

Text Mining in biology and biomedicine requires a large amount of domain-specific knowledge. Publicly accessible resources hold much of the information needed, yet their practical integration into natural language processing (NLP) systems is fraught with manifold hurdles, especially the problem of semantic disconnectedness throughout the various resources and components. Ontologies can provide the necessary framework for a consistent semantic integration, while additionally delivering formal reasoning capabilities to NLP.

In this chapter, we address four important aspects relating to the integration of ontology and NLP: (i) An analysis of the different integration alternatives and their respective vantages; (ii) The design requirements for an ontology supporting NLP tasks; (iii) Creation and initialization of an ontology using publicly available tools and databases; and (iv) The connection of common NLP tasks with an ontology, including technical aspects of ontology deployment in a text mining framework. A concrete application example—text mining of enzyme mutations—is provided to motivate and illustrate these points.

Keywords: Text Mining, NLP, Ontology Design, Ontology Population, Ontological NLP

Enhanced Semantic Access to the Protein Engineering Literature using Ontologies Populated by Text Mining

Abstract

The biomedical literature is growing at an ever-increasing rate, which pronounces the need to support scientists with advanced, automated means of accessing knowledge. We investigate a novel approach employing description logics (DL)-based queries made to formal ontologies that have been created using the results of text mining full-text research papers. In this paradigm, an OWL-DL ontology becomes populated with instances detected through natural language processing (NLP). The generated ontology can be queried by biologists using DL reasoners or integrated into bioinformatics workflows for further automated analyses. We demonstrate the feasibility of this approach with a system targeting the protein mutation literature.

Keywords: text mining; semantic web; ontological NLP; protein mutations; automated reasoning in bioinformatics; querying OWL-DL ontologies; description logics.

Automatic Traceability Recovery: An Ontological Approach

Abstract

Software maintainers routinely have to deal with a multitude of artifacts, like source code or documents. These artifacts often end up disconnected from each other, due to their different representations and levels of abstractions. One of the main challenges in software maintenance therefore is to recover and maintain the semantic connections among these artifacts. In this research, we present a novel approach that addresses this traceability issue by creating formal ontological representations for both software documentation and source code artifacts. The resulting representations are then aligned to establish traceability links at semantic level. Ontological queries and reasoning can be applied on these representations to infer and establish additional traceability links to support specific maintenance tasks.

Categories and Subject Descriptors: D2.7 [Distribution, Maintenance, and Enhancement]: Documentation, Restructuring, reverse engineering
General Terms: Software, Documentation, Management
Keywords: Ontologies, Traceability, Software Maintenance

Text Mining and Software Engineering: An Integrated Source Code and Document Analysis Approach

Syntaxtree

Abstract

Documents written in natural languages constitute a major part of the artifacts produced during the software engineering lifecycle. Especially during software maintenance or reverse engineering, semantic information conveyed in these documents can provide important knowledge for the software engineer. In this paper, we present a text mining system capable of populating a software ontology with information detected in documents. A particular novelty is the integration of results from automated source code analysis into an NLP pipeline, allowing to cross-link software artifacts represented in code and natural language on a semantic level.

Empowering Software Maintainers with Semantic Web Technologies

Achtung Seilbahn!

Abstract

Software maintainers routinely have to deal with a multitude of artifacts, like source code or documents, which often end up disconnected, due to their different representations and the size and complexity of legacy systems. One of the main challenges in software maintenance is to establish and maintain the semantic connections among all the different artifacts. In this paper, we show how Semantic Web technologies can deliver a unified representation to explore, query and reason about a multitude of software artifacts. A novel feature is the automatic integration of two important types of software maintenance artifacts, source code and documents, by populating their corresponding sub-ontologies through code analysis and text mining. We demonstrate how the resulting "Software Semantic Web" can support typical maintenance tasks through ontology queries and DL reasoning, such as security analysis, architectural evolution, and traceability recovery between code and documents.

Keywords: Software Maintenance, Ontology Population, Text Mining.

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