Open semantic annotation of scientific publications using DOMEO

<p>Abstract</p> <p>Background</p> <p>Our group has developed a useful shared software framework for performing, versioning, sharing and viewing Web annotations of a number of kinds, using an open representation model.</p> <p>Methods</p> <p>The Domeo Annotation Tool was developed in tandem with this open model, the Annotation Ontology (AO). Development of both the Annotation Framework and the open model was driven by requirements of several different types of alpha users, including bench scientists and biomedical curators from university research labs, online scientific communities, publishing and pharmaceutical companies.</p> <p>Several use cases were incrementally implemented by the toolkit. These use cases in biomedical communications include personal note-taking, group document annotation, semantic tagging, claim-evidence-context extraction, reagent tagging, and curation of textmining results from entity extraction algorithms.</p> <p>Results</p> <p>We report on the Domeo user interface here. Domeo has been deployed in beta release as part of the NIH Neuroscience Information Framework (NIF, <url>http://www.neuinfo.org</url><it/>) and is scheduled for production deployment in the NIF’s next full release.</p> <p>Future papers will describe other aspects of this work in detail, including Annotation Framework Services and components for integrating with external textmining services, such as the NCBO Annotator web service, and with other textmining applications using the Apache UIMA framework.</p

ASSESSING THE QUALITY OF SOFTWARE DEVELOPMENT TUTORIALS AVAILABLE ON THE WEB

Both expert and novice software developers frequently access software development resources available on the Web in order to lookup or learn new APIs, tools and techniques. Software quality is affected negatively when developers fail to find high-quality information relevant to their problem. While there is a substantial amount of freely available resources that can be accessed online, some of the available resources contain information that suffers from error proneness, copyright infringement, security concerns, and incompatible versions. Use of such toxic information can have a strong negative effect on developer’s efficacy. This dissertation focuses specifically on software tutorials, aiming to automatically evaluate the quality of such documents available on the Web. In order to achieve this goal, we present two contributions: 1) scalable detection of duplicated code snippets; 2) automatic identification of valid version ranges. Software tutorials consist of a combination of source code snippets and natural language text. The code snippets in a tutorial can originate from different sources, perhaps carrying stringent licensing requirements or known security vulnerabilities. Developers, typically unaware of this, can reuse these code snippets in their project. First, in this thesis, we present our work on a Web-scale code clone search technique that is able to detect duplicate code snippets between large scale document and source code corpora in order to trace toxic code snippets. As software libraries and APIs evolve over time, existing software development tutorials can become outdated. It is difficult for software developers and especially novices to determine the expected version of the software implicit in a specific tutorial in order to decide whether the tutorial is applicable to their software development environment. To overcome this challenge, in this thesis we present a novel technique for automatic identification of the valid version range of software development tutorials on the Web

Enabling Flexibility in Process-Aware Information Systems: Challenges, Methods, Technologies

In today’s dynamic business world, the success of a company increasingly depends on its ability to react to changes in its environment in a quick and flexible way. Companies have therefore identified process agility as a competitive advantage to address business trends like increasing product and service variability or faster time to market, and to ensure business IT alignment. Along this trend, a new generation of information systems has emerged—so-called process-aware information systems (PAIS), like workflow management systems, case handling tools, and service orchestration engines. With this book, Reichert and Weber address these flexibility needs and provide an overview of PAIS with a strong focus on methods and technologies fostering flexibility for all phases of the process lifecycle (i.e., modeling, configuration, execution and evolution). Their presentation is divided into six parts. Part I starts with an introduction of fundamental PAIS concepts and establishes the context of process flexibility in the light of practical scenarios. Part II focuses on flexibility support for pre-specified processes, the currently predominant paradigm in the field of business process management (BPM). Part III details flexibility support for loosely specified processes, which only partially specify the process model at build-time, while decisions regarding the exact specification of certain model parts are deferred to the run-time. Part IV deals with user- and data-driven processes, which aim at a tight integration of processes and data, and hence enable an increased flexibility compared to traditional PAIS. Part V introduces existing technologies and systems for the realization of a flexible PAIS. Finally, Part VI summarizes the main ideas of this book and gives an outlook on advanced flexibility issues. The attached pdf file gives a preview on Chapter 3 of the book which explains the book's overall structure

Heuristics Miners for Streaming Event Data

More and more business activities are performed using information systems. These systems produce such huge amounts of event data that existing systems are unable to store and process them. Moreover, few processes are in steady-state and due to changing circumstances processes evolve and systems need to adapt continuously. Since conventional process discovery algorithms have been defined for batch processing, it is difficult to apply them in such evolving environments. Existing algorithms cannot cope with streaming event data and tend to generate unreliable and obsolete results. In this paper, we discuss the peculiarities of dealing with streaming event data in the context of process mining. Subsequently, we present a general framework for defining process mining algorithms in settings where it is impossible to store all events over an extended period or where processes evolve while being analyzed. We show how the Heuristics Miner, one of the most effective process discovery algorithms for practical applications, can be modified using this framework. Different stream-aware versions of the Heuristics Miner are defined and implemented in ProM. Moreover, experimental results on artificial and real logs are reported

Principles in Patterns (PiP) : Institutional Approaches to Curriculum Design Institutional Story

The principal outputs of the PiP Project surround the Course and Class Approval (C-CAP) system. This web-based system built on Microsoft SharePoint addresses and resolves many of the issues identified by the project. Generally well received by both academic and support staff, the system provides personalised views, adaptive forms and contextualised support for all phases of the approval process. Although the system deliberately encapsulates and facilitates existing approval processes thus achieving buy-in, it is already achieving significant improvements over the previous processes, not only in reducing the administrative overheads but also in supporting curriculum design and academic quality. The system is now embedded across three faculties and is now considered by the University of Strathclyde to be a "core institutional service". Alongside the C-CAP system the PiP Project also cultivated a suite of approaches: an incremental systems development methodology; a structured and replicable evaluation approach, and; Strathclyde's Lean Approach to Efficiencies in Education Kit (SLEEK) business process improvement methodology Each is based on recognised formal techniques, providing the basis for a rigorous approach. This is contextualised within and adapted to the HE institutional context thus building the foundation not only for the project but ultimately for institution wide process improvement. This "institutional story" report summarises the principal outcomes of the Project

requirements and use cases

In this report, we introduce our initial vision of the Corporate Semantic Web as the next step in the broad field of Semantic Web research. We identify requirements of the corporate environment and gaps between current approaches to tackle problems facing ontology engineering, semantic collaboration, and semantic search. Each of these pillars will yield innovative methods and tools during the project runtime until 2013. 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. We propose an initial layout for an integrative architecture of a Corporate Semantic Web provided by these three core pillars

Versioning in Interactive Systems

Dealing with past states of an interactive system is often difficult, and users often resort to unwieldy methods such as saving and naming multiple copies. Versioning tools can help users save and manipulate different versions of a document, but traditional tools designed for coding are often unsuitable for interactive systems. Supporting versioning in interactive systems requires investigation of how users think about versions and how they want to access and manipulate past states. We first surveyed users to understand what a ‘version’ means to them in the context of digital interactive work, and the circumstances under which they create new versions or go back to previous ones. We then built a versioning tool that can store versions using a variety of explicit and implicit mechanisms and shows a graphical representation of the version tree to allow easy inspection and manipulation. To observe how users used versions in different work contexts, we tested our versioning tool in two interactive systems – a game level editor and a web analysis tool. We report several new findings about how users of interactive systems create versions and use them as undo alternatives, exploring options, and planning future work. Our results show that versioning can be a valuable component that improves the power and usability of interactive systems. The new understanding that we gained about versioning in interactive environments by developing and evaluating our custom version tool can help us design more effective versioning tools for interactive systems