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[STORY] Capture and output list of relevant citations associated with each pipeline #49

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tclose opened this issue Mar 28, 2022 · 1 comment
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analysis-design Complex analysis workflow epic mid-level Requires moderate framework/domain-specific knowledge pipelines story a unit of work
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@tclose
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tclose commented Mar 28, 2022

Description

As a pipelines user, I would like to be able to access a lit of citations corresponding to the methods used in a pipeline and a short description of how they fit together (e.g. dot-points), so that I can write my methods section.

As a pipeline developer, I would like users to be prompted to acknowledge the work put into designing the pipeline as well as all the methods it builds upon, so that my work and that of the methods developers is appropriately recognised.

Acceptance Criteria

  • 1. Citations are recorded alongside pipeline implementation
  • 2. Compiled lists of citations are saved next to generated derivatives
  • 3. Links to the compiled list are prominent in the XNAT UI

Thoughts

  • A Zenodo reference to the pipeline software itself, including versioning (will have to think about the best way to do this)
  • Any paper that describes the synthesised workflow
  • Papers that describe the component parts of the workflow (we may need to be clever about how we do this to avoid generating a huge list)
  • Software used (e.g. FSL, MRtrix, Pydra, Arcana, ...)
  • Acknowledgements of AIS, NIF node, etc...

The idea would be to also capture how the reference was used so we can kind of generate a dot-point methods markdown document that gets saved alongside the generated derivatives.

Probably it makes sense to define this in the pipeline decorator, e.g.

@analysis(Clinical)
class Bold():

    fmri: NiftiXGz
    preprocessed: NiftiXGz

    @pipeline(preprocessed,
              citations=[
                  Citation(doi='https://doi.org/10.1038/s41592-018-0235-4',
                           desc="draws upon the methods and default parameters used in fMRIPrep")])
    def preprocess(self, wf, fmri):
        ...
@tclose tclose added this to the 2.0.0b milestone Mar 28, 2022
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tclose commented Jun 19, 2022

@tclose tclose moved this to Backlog in AIS Master Project Jun 20, 2022
@tclose tclose added story a unit of work incomplete-desc and removed analysis-class labels Jun 21, 2022
@tclose tclose changed the title Capture and output list of relevant citations associated with each pipeline [STORY] Capture and output list of relevant citations associated with each pipeline Jun 21, 2022
@tclose tclose added mid-level Requires moderate framework/domain-specific knowledge analysis-design Complex analysis workflow epic and removed incomplete-desc labels Jun 21, 2022
@tclose tclose added the ready label Aug 1, 2022
@tclose tclose removed the ready label Aug 10, 2022
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