- Goal: to establish an understanding of the capabilities of available provenance-related systems
- The representations that systems use to document details of processes that have occurred
- The capabilities of each system in answering provenance-related queries
- What each system considers to be within scope of the topic of provenance (regardless of whether the system can yet achieve all problems in that scope)
- Challenge
- Run a workflow for an fMRI application
- Answer a set of queries over the provenance derived
- Example workflow
#!/bin/sh AIR5.2.5/bin/align_warp anatomy1.img reference.img warp1.warp -m 12 -q AIR5.2.5/bin/align_warp anatomy2.img reference.img warp2.warp -m 12 -q AIR5.2.5/bin/align_warp anatomy3.img reference.img warp3.warp -m 12 -q AIR5.2.5/bin/align_warp anatomy4.img reference.img warp4.warp -m 12 -q AIR5.2.5/bin/reslice warp1.warp resliced1 AIR5.2.5/bin/reslice warp2.warp resliced2 AIR5.2.5/bin/reslice warp3.warp resliced3 AIR5.2.5/bin/reslice warp4.warp resliced4 AIR5.2.5/bin/softmean atlas.hdr y null resliced1.img resliced2.img resliced3.img resliced4.img fsl/bin/slicer atlas.hdr -x .5 atlas-x.pgm fsl/bin/slicer atlas.hdr -y .5 atlas-y.pgm fsl/bin/slicer atlas.hdr -z .5 atlas-z.pgm convert atlas-x.pgm atlas-x.gif convert atlas-y.pgm atlas-y.gif convert atlas-z.pgm atlas-z.gif
- Core provenance queries
- Find the process that led to Atlas X Graphic / everything that caused Atlas X Graphic to be as it is. This should tell us the new brain images from which the averaged atlas was generated, the warping performed etc.
- Find the process that led to Atlas X Graphic, excluding everything prior to the averaging of images with softmean.
- Find the Stage 3, 4 and 5 details of the process that led to Atlas X Graphic.
- Find all invocations of procedure align_warp using a twelfth order nonlinear 1365 parameter model (see model menu describing possible values of parameter “-m 12” of align_warp) that ran on a Monday.
- Find all Atlas Graphic images outputted from workflows where at least one of the input Anatomy Headers had an entry
global maximum=4095. The contents of a header file can be extracted as text using the scanheader AIR utility. - Find all output averaged images of softmean (average) procedures, where the warped images taken as input were align_warped using a twelfth order nonlinear 1365 parameter model, i.e. “where softmean was preceded in the workflow, directly or indirectly, by an align_warp procedure with argument -m 12.”
- A user has run the workflow twice, in the second instance replacing each procedures (convert) in the final stage with two procedures: pgmtoppm, then pnmtojpeg. Find the differences between the two workflow runs. The exact level of detail in the difference that is detected by a system is up to each participant.
- A user has annotated some anatomy images with a key-value pair
center=UChicago. Find the outputs of align_warp where the inputs are annotated withcenter=UChicago. - A user has annotated some atlas graphics with key-value pair where the key is
studyModality. Find all the graphical atlas sets that have metadata annotationstudyModalitywith valuesspeech,visualoraudio, and return all other annotations to these files.