Use Case: Link Papers to Script and Model Runs

[rayi113]

Use Case: Link Papers to Script Runs and scripts

• Contributors: Matt Jones (@mbjones), Chris Jones (@csjx)

  Goal and Summary

A scientist can provide citation links to scholarly papers that were derived from particular executions of a script or model. These links can take the form of links to published identifiers for the execution trace, or from the trace to the paper via e.g., a DOI. As a scientist using e.g., R or Matlab, The goal is to link a paper to a given script run to document the exact process used to derive published data, figures, or tables. In R or Matlab, after executing a script and recording provenance information about the run, a researcher can later update the execution's provenance information by providing a link to a permanent identifier (such as a DOI) of a published document. Other researchers can discover the papers from links of the script executions.

Why is it important and to whom?

• It is critical to computational reproducibility

• It improves discovery via finding all papers related to particular analyses

  Why hasn’t it been solved yet?

• Repositories for execution traces are rare, and those that exist are not well established

• Tools for generating execution traces are not widely adopted

• Standards for representing traces have been in flux (e.g., OPM, PROV, etc)

  Actionable Outcomes

• Additional Information and Links

• DataONE Use Case 42A: Link Papers to Script Runs

[alesarrett]

Could the "Code as a research object" project (https://github.com/mozillascience/code-research-object) from Mozillascience be a useful tool?

[mbjones]

@alesarrett Yes, absolutely. See the work we've already done as part of that project in my codemeta repository, which has crosswalks among existing software metadata efforts and a proposed JSON-LD context for software metadata. We also have a working PROV extension in DataONE. For an example of the kind of provenance tracing I think needs to be widespread, see the Ma et al. paper titled Capturing provenance of global change information, doi:10.1038/nclimate2141.