The Virtual Skeleton Database: An Open Access Repository for Biomedical Research and Collaboration

Background: Statistical shape models are widely used in biomedical research. They are routinely implemented for automatic image segmentation or object identification in medical images. In these fields, however, the acquisition of the large training datasets, required to develop these models, is usually a time-consuming process. Even after this effort, the collections of datasets are often lost or mishandled resulting in replication of work. Objective: To solve these problems, the Virtual Skeleton Database (VSD) is proposed as a centralized storage system where the data necessary to build statistical shape models can be stored and shared. Methods: The VSD provides an online repository system tailored to the needs of the medical research community. The processing of the most common image file types, a statistical shape model framework, and an ontology-based search provide the generic tools to store, exchange, and retrieve digital medical datasets. The hosted data are accessible to the community, and collaborative research catalyzes their productivity. Results: To illustrate the need for an online repository for medical research, three exemplary projects of the VSD are presented: (1) an international collaboration to achieve improvement in cochlear surgery and implant optimization, (2) a population-based analysis of femoral fracture risk between genders, and (3) an online application developed for the evaluation and comparison of the segmentation of brain tumors. Conclusions: The VSD is a novel system for scientific collaboration for the medical image community with a data-centric concept and semantically driven search option for anatomical structures. The repository has been proven to be a useful tool for collaborative model building, as a resource for biomechanical population studies, or to enhance segmentation algorithms.

Digital Repository, Institutional Repository, DigitalCommons

The University of Texas School of Nursing at Houston and HAM-TMC Library discuss the benefits of an institutional repository, DigitalCommons, and cover initial steps to create accounts and publish to the institutions DigitalCommons.

Use of an Online Photo Management and Sharing Application to Create a Searchable Digital Dental Radiograph Repository

Problem: Dental radiographs generally display one or more findings/diagnoses, and are linked to a unique set of patient demographics, medical history and other findings not represented by the image. However, this information is not associated with radiographs in any type of meta format, and images are not searchable based on any clinical criteria (1,2). The purpose of this pilot study is to create an online, searchable data repository of dental radiographs to be used for patient care, teaching and research. [See PDF for complete abstract]

Institutional Repository Workflow from Initial Inquiry to Repository Upload

A workflow flowchart on the verification steps involved in preparation to uploading assets to the University of Connecticut's institutional repository (http://digitalcommons.uconn.edu). This flowchart is geared towards assisting subject liaisons who also serve as series administrators for UConn@DigitalCommons.

Google Analytics & CONTENTdm: Harness Up Your Repository Metrics

A demonstration of the installation and use of Google Analytics with CONTENTdm in order to better gather metrics and insight into both general and specific online traffic across such digital repositories. Issues addressed will include collection-level traffic, digital object-level traffic, general site referrals to the repository, specific referrals to the repository, search engine referrals, user keywords, traffic occurring inside and/or outside an institution’s own network, reporting options.

Digital repository implementation: a toolbox for streamlined success

Purpose – The purpose of this paper is to describe the tools and strategies that were employed by C/W MARS to successfully develop and implement the Digital Treasures digital repository. Design/methodology/approach – This paper outlines the planning and subsequent technical issues that arise when implementing a digitization project on the scale of the large, multi-type, automated library network. Workflow solutions addressed include synchronous online metadata record submissions from multiple library sources and the delivery of collection-level use statistics to participating library administrators. The importance of standards-based descriptive metadata and the role of project collaboration are also discussed. Findings – From the time of its initial planning, the Digital Treasures repository was fully implemented in six months. The discernable and statistically quantified online discovery and access of actual digital objects greatly assisted libraries unsure of their own staffing costs/benefits to join the repository. Originality/value – This case study may serve as a possible example of initial planning, workflow and final implementation strategies for new repositories in both the general and library consortium environment. Keywords – Digital repositories, Library networks, Data management. Paper type – Case study

Aiming at improving access to research output through the institutional repository

The paper is to introduce the institutional repository (IR) as a powerful tool to support the researchers of the institution to archive and disseminate their research findings freely to the scholarly community on the Internet. The IR can improve the access to an institution’s research output enormously. The operations of an IR also require various interactions with researchers, which enables the library to gain a solid understanding of research needs and expectations. Through such interaction, the relationship and mutual trust between researchers and the library are strengthened. The experiences of the Institute of Developing Economies (IDE) library can be useful to other special libraries.

A repository for integration of software artifacts with dependency resolution and federation support

While developing new IT products, reusability of existing components is a key aspect that can considerably improve the success rate. This fact has become even more important with the rise of the open source paradigm. However, integrating different products and technologies is not always an easy task. Different communities employ different standards and tools, and most times is not clear which dependencies a particular piece of software has. This is exacerbated by the transitive nature of these dependencies, making component integration a complicated affair. To help reducing this complexity we propose a model-based repository, capable of automatically resolve the required dependencies. This repository needs to be expandable, so new constraints can be analyzed, and also have federation support, for the integration with other sources of artifacts. The solution we propose achieves these working with OSGi components and using OSGi itself.