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Use Case: Link Papers to Script and Model Runs #1

rayi113 opened this Issue Jan 16, 2015 · 2 comments


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rayi113 commented Jan 16, 2015

Use Case: Link Papers to Script Runs and scripts

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


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alesarrett commented Jan 26, 2015

Could the "Code as a research object" project ( from Mozillascience be a useful tool?


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mbjones commented Jan 26, 2015

@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.

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