OntoMaven: Maven-based Ontology Development and Management of Distributed Ontology Repositories

In collaborative agile ontology development projects support for modular reuse of ontologies from large existing remote repositories, ontology project life cycle management, and transitive dependency management are important needs. The Apache Maven approach has proven its success in distributed collaborative Software Engineering by its widespread adoption. The contribution of this paper is a new design artifact called OntoMaven. OntoMaven adopts the Maven-based development methodology and adapts its concepts to knowledge engineering for Maven-based ontology development and management of ontology artifacts in distributed ontology repositories.Comment: Pre-print submission to 9th International Workshop on Semantic Web Enabled Software Engineering (SWESE2013). Berlin, Germany, December 2-5, 201

Git4Voc: Git-based Versioning for Collaborative Vocabulary Development

Collaborative vocabulary development in the context of data integration is the process of finding consensus between the experts of the different systems and domains. The complexity of this process is increased with the number of involved people, the variety of the systems to be integrated and the dynamics of their domain. In this paper we advocate that the realization of a powerful version control system is the heart of the problem. Driven by this idea and the success of Git in the context of software development, we investigate the applicability of Git for collaborative vocabulary development. Even though vocabulary development and software development have much more similarities than differences there are still important differences. These need to be considered within the development of a successful versioning and collaboration system for vocabulary development. Therefore, this paper starts by presenting the challenges we were faced with during the creation of vocabularies collaboratively and discusses its distinction to software development. Based on these insights we propose Git4Voc which comprises guidelines how Git can be adopted to vocabulary development. Finally, we demonstrate how Git hooks can be implemented to go beyond the plain functionality of Git by realizing vocabulary-specific features like syntactic validation and semantic diffs

Ontology Summit 2008 Communiqué: Towards an open ontology repository

Each annual Ontology Summit initiative makes a statement appropriate to each Summits theme as part of our general advocacy designed to bring ontology science and engineering into the mainstream. The theme this year is "Towards an Open Ontology Repository". This communiqué represents the joint position of those who were engaged in the year's summit discourse on an Open Ontology Repository (OOR) and of those who endorse below. In this discussion, we have agreed that an "ontology repository is a facility where ontologies and related information artifacts can be stored, retrieved and managed." We believe in the promise of semantic technologies based on logic, databases and the Semantic Web, a Web of exposed data and of interpretations of that data (i.e., of semantics), using common standards. Such technologies enable distinguishable, computable, reusable, and sharable meaning of Web and other artifacts, including data, documents, and services. We also believe that making that vision a reality requires additional supporting resources and these resources should be open, extensible, and provide common services over the ontologies

Ontology Repositories

The growing use and application of ontologies in the last years has led to an increased interest of researchers and practitioners in the development of ontologies, either from scratch o by reusing existing ones. ..

concept paper

In this concept paper, we outline our working plan for the next phase of the Corporate Semantic Web project. The plan covers the period from March 2009 to March 2010. Corporate ontology engineering will improve the facilitation of agile ontology engineering to lessen the costs of ontology development and, especially, maintenance. Corporate semantic collaboration focuses the human- centered aspects of knowledge management in corporate contexts. Corporate semantic search is settled on the highest application level of the three research areas and at that point it is a representative for applications working on and with the appropriately represented and delivered background knowledge. Each of these pillars will yield innovative methods and tools during the project runtime until 2013. We propose a concept draft and a working plan covering the next twelve months for an integrative architecture of a Corporate Semantic Web provided by these three core pillars

A Lightweight Framework for Universal Fragment Composition

Domain-specific languages (DSLs) are useful tools for coping with complexity in software development. DSLs provide developers with appropriate constructs for specifying and solving the problems they are faced with. While the exact definition of DSLs can vary, they can roughly be divided into two categories: embedded and non-embedded. Embedded DSLs (E-DSLs) are integrated into general-purpose host languages (e.g. Java), while non-embedded DSLs (NE-DSLs) are standalone languages with their own tooling (e.g. compilers or interpreters). NE-DSLs can for example be found on the Semantic Web where they are used for querying or describing shared domain models (ontologies). A common theme with DSLs is naturally their support of focused expressive power. However, in many cases they do not support non–domain-specific component-oriented constructs that can be useful for developers. Such constructs are standard in general-purpose languages (procedures, methods, packages, libraries etc.). While E-DSLs have access to such constructs via their host languages, NE-DSLs do not have this opportunity. Instead, to support such notions, each of these languages have to be extended and their tooling updated accordingly. Such modifications can be costly and must be done individually for each language. A solution method for one language cannot easily be reused for another. There currently exist no appropriate technology for tackling this problem in a general manner. Apart from identifying the need for a general approach to address this issue, we extend existing composition technology to provide a language-inclusive solution. We build upon fragment-based composition techniques and make them applicable to arbitrary (context-free) languages. We call this process for the composition techniques’ universalization. The techniques are called fragment-based since their view of components— reusable software units with interfaces—are pieces of source code that conform to an underlying (context-free) language grammar. The universalization process is grammar-driven: given a base language grammar and a description of the compositional needs wrt. the composition techniques, an adapted grammar is created that corresponds to the specified needs. The result is thus an adapted grammar that forms the foundation for allowing to define and compose the desired fragments. We further build upon this grammar-driven universalization approach to allow developers to define the non–domain-specific component-oriented constructs that are needed for NE-DSLs. Developers are able to define both what those constructs should be, and how they are to be interpreted (via composition). Thus, developers can effectively define language extensions and their semantics. This solution is presented in a framework that can be reused for different languages, even if their notion of ‘components’ differ. To demonstrate the approach and show its applicability, we apply it to two Semantic Web related NE-DSLs that are in need of component-oriented constructs. We introduce modules to the rule-based Web query language Xcerpt and role models to the Web Ontology Language OWL

Bioconductor: open software development for computational biology and bioinformatics.

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples