Discuss what we will consider a GPF

New Frameworks to Create a New Generation of Scientific Articles

Several frameworks have been developed to document scientific articles so that they are more useful to researchers than just a simple PDF. These include iPython Notebook, Weaver (for R), etc.

Elsevier has invested in some initiatives in this direction. They carried out an Executable Papers Challenge. They have a new type of paper called a software paper.

The Case of the Tuberculosis Drugome

This is a case where a workflow system was used to make data and software explicit and published as linked open data in RDF (i.e., accessible Web objects in the Semantic Web). The data were assigned DOIs, as was the workflow.

• the original "drugome" paper
• the web site that describes how that paper was reproduced
• detailed documentation of the drugome method
• a publication that reports on that work.

Looking at the Future

The Vision

In the future, scientists will use radically new tools to generate papers. As scientists do their work, those tools will be documenting the work and all the associated digital objects (data, software, etc) so that when it comes time to publish a paper everything will be easily documented and included. Today, several research tools exist for working in this way, but they are not routinely used and sometimes they do not always fit the scientist research workflow.

In the future, publishers will accept submissions that do not just contain PDF but also data, software, and other digital objects relevant to the research. Today, many journals accept datasets together with papers, some journals accept software and software papers, but no journal includes the full details of the data, software, workflow, and visualizations of a paper.

In the future, readers of papers will be able to interact with the paper document, modify its figures to explore the data, reproduce the results, run the method with new data. Today, readers simply get a static paper, and even if the data is available they have to download it and analyze it themselves.

In the future, data producers and software developers will get credit for the work that they do because all publications that build on their work will acknowledge their work through citations. Today, there is limited credit and reward for those that create data and software.

What is a Geoscience Paper of the Future?

A GPF paper includes:

• data: documented, described in a public repository, has a license specified and is open if possible, and cited with DOIs
• software: documented, in a public repository, has a license specified and is open source if possible, and cited with DOIs
• provenance: explicitly documented as a workflow sketch, a formal workflow, or a provenance record (in PROV or similar standard), possibly in a shared repository and given a DOI
• figures/visualizations: generated by explicit code and are the result of a workflow or provenance record