Using the Drupal Content Management Software (CMS) as a framework for OMICS/Imaging-based collaboration

Content: FaceBase, a collaborative project of craniofacial researchers, is developing a comprehensive repository of the genetics underlying midfacial development. When complete, the FaceBase Hub will include multiple types of human and animal model data (including images, genotypes, expression analysis, and sequence data), a comprehensive set of web-based tools for mining the databases, a forum for connections between investigators to enable enhanced research opportunities, access to translational research including a bio-repository, as well as genetics tools and mouse strains for clefting research.   Technology: Drupal, an open-source Content Management Software (CMS) tool, serves as the platform for development of the FaceBase web portal. Design: It provides flexible, configurable support for standard web facilities (user account management, uploading data, searching and browsing capabilities, annotation tools, publications archive, etc), via a broad range of open-source, freely available modules that can be easily installed and customized. Drupal and its extensive module library effectively provide a low-cost core foundation, freeing resources for the development of functionality (in the form of new modules) specific to scientific needs. One of the goals of the FaceBase effort is to develop a general model of the software components needed to support bioinformatics data portals, which can then be applied to building portals serving other areas of research. Results: Building on the software engineering community’s work in design patterns, we are developing a set of abstract pattern descriptions of the various classes of functionality required for sites such as FaceBase. Conclusions: These descriptions, implemented by a set of Drupal modules, will provide infrastructure that will both support and facilitate basic science, clinical, and translational research and advance data sharing to facilitate research in cleft palate and lip abnormalities.

Drupal Content Management System Open-source Content Management Software (CMS) tool Flexible, configurable support for standard web facilities Easily installable and customizable modules: Resources for the development of functionality specific to users needs Platform for several collaborative web portals

Architecture

URL: www.facebase.org

Diverse Projects

Gene Wiki

User Forums

Custom Data Upload

Custom Image View

Technology Probes Hutchinson, et al, 2003 Prototypes designed to elicit responses and promote discussion

Technology Probe: Linked Data

Technology Probe: Literature Search

Technology Probe: Annotating Images

Technology Probe: Gene Atlas

Contact Us: help.facebase@gmail.com Ketaki Desai, Ph.D. Dept. of Biomedical Informatics University of Pittsburgh desaikv@upmc.edu