Building biomedical web communities using a semantically aware content management system

Abstract

Web-based biomedical communities are becoming an increasingly popular vehicle for sharing information amongst researchers and are fast gaining an online presence. However, information organization and exchange in such communities is usually unstructured, rendering interoperability between communities difficult. Furthermore, specialized software to create such communities at low cost-targeted at the specific common information requirements of biomedical researchers-has been largely lacking. At the same time, a growing number of biological knowledge bases and biomedical resources are being structured for the Semantic Web. Several groups are creating reference ontologies for the biomedical domain, actively publishing controlled vocabularies and making data available in Resource Description Framework (RDF) language. We have developed the Science Collaboration Framework (SCF) as a reusable platform for advanced structured online collaboration in biomedical research that leverages these ontologies and RDF resources. SCF supports structured 'Web 2.0' style community discourse amongst researchers, makes heterogeneous data resources available to the collaborating scientist, captures the semantics of the relationship among the resources and structures discourse around the resources. The first instance of the SCF framework is being used to create an open-access online community for stem cell research-StemBook (http://www.stembook.org). We believe that such a framework is required to achieve optimal productivity and leveraging of resources in interdisciplinary scientific research. We expect it to be particularly beneficial in highly interdisciplinary areas, such as neurodegenerative disease and neurorepair research, as well as having broad utility across the natural sciences.

Data Citation as a Bibliometric Oxymoron

“…Discovery can be improved by more extensive description of data, figures, tables, and other elements in publications. Such descriptions can be accommodated by open annotation systems that facilitate interoperability across systems, which includes synchronizing links to related resources (Ciccarese, Ocana, & Clark, 2012;Das et al, 2009;Foster & Moreau, 2006;Hunter, 2009;Van de Sompel et al, 2012). These approaches may be effective to the extent that document enrichment survives the publication process.…”

Produce and Consume Linked Data with Drupal!

“…As for pre-existing work specifically in Drupal, a recent paper [8] describes the related SCF (Science Collaboration Framework) Node Proxy architecture. This module, developed specifically for biomedical applications, enables RDF from defined SPARQL queries to be mapped to specific Drupal content types.…”

“…This is encouraging. Our module is currently being tested and will be deployed in the next version of the Science Collaboration Framework (SCF) platform, a special Drupal distribution developed at the Massachusetts General Hospital and Harvard University in collaboration with DERI and other participating institutions [8].…”

“…The Science Collaboration Framework (SCF) [8] is a distributed Drupal installation launched in Beta version at various institutions working in the Biomedical domain.…”

Research Collaboration Tools: A Resource Guide for Medical Librarians

“…Because of this, a number of resources have emerged to help facilitate collaboration between researchers (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11). What tools, then, are available to help in the tasks of finding collaborators, carrying out work, or sharing information and expertise?…”