The p-medicine Workbench

The p-medicine Workbench is the end-user application that provides access to various p-medicine tools for use by clinicians. This tool is basically an “application store” where different applications, tools, and services are categorized and indexed together with information about their functionality, operation, development status, accessibility, etc. The primary users of this application are clinicians but of course it can also be useful to other user groups such as bioinformaticians, etc.

The Workbench aims to boost the communication and collaboration of researchers among Europe for the machine-assisted sharing of expertise. It is a web-based integrated and collaborative environment where tools relevant to p-medicine can be discovered, published and annotated semantically and with proper metadata. The fact that the Workbench is a portlet, makes it part of the p-medicine portal. Consequently,  the Workbench can be accessed via

The end-users can search for tools of their interest by semantically asking the Workbench about what exactly they need. The system will answer with a list of tools and publications that semantically make sense with regard to the question. To guarantee this, the Workbench uses the EDAM ontology. EDAM stands for “EMBRACE Data and Methods” and constitutes an ontology of common bioinformatics operations, topics, types of data including identifiers, and formats.

Existing tools hosted by the Workbench’s repository can be annotated with proper metadata and ontology terms. The metadata to be used for annotating a tool include specific information of the tool (name, description, etc.), particular tags specified by the user, certain categories that further classify the tool, and the source code of the tool (if this is anticipated). Finally, the semantic annotation of the tools means that the connection of a tool with specific ontology terms is established. The system is designed in such a way that it assists the user to select the most appropriate ontology terms by recommending and justifying them.

End-users can register new tools through the Workbench, which will be available to other users through the tool discovery phase. When registering a new tool, the user can also annotate it in the same way as mentioned above. Newly registered tools are not immediately available to the public. Instead, a user with specific user role will confirm them first and then categorize them as discoverable.

These three functional capabilities are not the only ones provided by the Workbench. The users may also mark any tool as “favorite” and put it on their personal list of favorite Tools.