bdbms -- A Database Management System for Biological Data

Biologists are increasingly using databases for storing and managing their data. Biological databases typically consist of a mixture of raw data, metadata, sequences, annotations, and related data obtained from various sources. Current database technology lacks several functionalities that are needed by biological databases. In this paper, we introduce bdbms, an extensible prototype database management system for supporting biological data. bdbms extends the functionalities of current DBMSs to include: (1) Annotation and provenance management including storage, indexing, manipulation, and querying of annotation and provenance as first class objects in bdbms, (2) Local dependency tracking to track the dependencies and derivations among data items, (3) Update authorization to support data curation via content-based authorization, in contrast to identity-based authorization, and (4) New access methods and their supporting operators that support pattern matching on various types of compressed biological data types. This paper presents the design of bdbms along with the techniques proposed to support these functionalities including an extension to SQL. We also outline some open issues in building bdbms.Comment: This article is published under a Creative Commons License Agreement (http://creativecommons.org/licenses/by/2.5/.) You may copy, distribute, display, and perform the work, make derivative works and make commercial use of the work, but, you must attribute the work to the author and CIDR 2007. 3rd Biennial Conference on Innovative Data Systems Research (CIDR) January 710, 2007, Asilomar, California, US

The Evolution of myExperiment

The myExperiment social website for sharing scientific workflows, designed according to Web 2.0 principles, has grown to be the largest public repository of its kind. It is distinctive for its focus on sharing methods, its researcher-centric design and its facility to aggregate content into sharable 'research objects'. This evolution of myExperiment has occurred hand in hand with its users. myExperiment now supports Linked Data as a step toward our vision of the future research environment, which we categorise here as '3rd generation e-Research'

Survey of tools for collaborative knowledge construction and sharing

The fast growth and spread of Web 2.0 environments have demonstrated the great willingness of general Web users to contribute and share various type of content and information. Many very successful web sites currently exist which thrive on the wisdom of the crowd, where web users in general are the sole data providers and curators. The Semantic Web calls for knowledge to be semantically represented using ontologies to allow for better access and sharing of data. However, constructing ontologies collaboratively is not well supported by most existing ontology and knowledge-base editing tools. This has resulted in the recent emergence of a new range of collaborative ontology construction tools with the aim of integrating some Web 2.0 features into the process of structured knowledge construction. This paper provides a survey of the start of the art of these tools, and highlights their significant features and capabilities

Supporting Collaborative Health Tracking in the Hospital: Patients' Perspectives

The hospital setting creates a high-stakes environment where patients' lives depend on accurate tracking of health data. Despite recent work emphasizing the importance of patients' engagement in their own health care, less is known about how patients track their health and care in the hospital. Through interviews and design probes, we investigated hospitalized patients' tracking activity and analyzed our results using the stage-based personal informatics model. We used this model to understand how to support the tracking needs of hospitalized patients at each stage. In this paper, we discuss hospitalized patients' needs for collaboratively tracking their health with their care team. We suggest future extensions of the stage-based model to accommodate collaborative tracking situations, such as hospitals, where data is collected, analyzed, and acted on by multiple people. Our findings uncover new directions for HCI research and highlight ways to support patients in tracking their care and improving patient safety

The myExperiment Open Repository for Scientific Workflows

4th International Conference on Open RepositoriesThis presentation was part of the session : Conference PresentationsDate: 2009-05-19 10:00 AM – 11:30 AMmyExperiment is an open repository solution for the born-digital items arising in contemporary research practice, in particular scientific workflows and experiment plans. Launched in November 2007, the public repository (myexperiment.org) has established a significant collection of scientific workflows, spanning multiple disciplines and multiple workflow systems, which has been accessed by over 16,000 users worldwide. Built according to Web 2.0 design principles, myExperiment demonstrates the success of blending modern social curation methods with the demands of researchers sharing hard-won intellectual assets and research works within a scholarly communication lifecycle. myExperiment is an important component in the revolution in creating, sharing and publishing scientific results, and has already established itself as a valuable and unique repository with a growing international presence.JISC; EPSRC; Microsoft Corporatio

Issues for the sharing and re-use of scientific workflows

In this paper, we outline preliminary findings from an ongoing study we have been conducting over the past 18 months of researchers’ use of myExperiment, a Web 2.0-based repository with a focus on social networking around shared research artefacts such as workflows. We present evidence of myExperiment users’ workflow sharing and re-use practices, motivations, concerns and potential barriers. The paper concludes with. a discussion of the implications of these our findings for community formation, diffusion of innovations, emerging drivers and incentives for research practice, and IT systems design