PMR2: supporting collaborative, reproducible, and discoverable science
My poster from the ICSB 2014 meeting.
Background: PMR2 is the software framework supporting the Physiome Repository (https://models.physiomeproject.org). All content of the Physiome Repository is stored in version-controlled workspaces and specific revisions of a workspace can be exposed with a persistent URL and customisable presentation via the web interface. Access control is a key part of PMR2 and users of the Physiome Repository are able to choose to keep their data private, shared with specific collaborators, or public.
Method: Recent developments in the PMR2 software stack have seen the inclusion of semantic web technologies and the provision of new web services that are able to leverage the semantic content of the Physiome Repository to enhance the ability of application developers to discover, access, and modify data contained in the Physiome Repository.
Results: Users of the Physiome Repository are now able to flag specific items in their workspaces as annotations to be indexed in the semantic knowledgebase of the repository. When new versions of these items are pushed into the workspace, the knowledgebase is automatically updated. Application developers are able to make use of PMR2 web services to access this semantic knowledgebase to discover data matching their requirements.
Conclusion: PMR2 provides a framework encouraging the collaborative development and evolution of mathematical models and associated data. Recent innovation in the PMR2 framework has significantly improved the ability of application developers and repository users to discover content that meets their requirements.