2013-05-29 Taverna Provenance (pptx source)
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Slide deck presenting the Provenance support of Taverna workflow system, detailing architecture, ontologies and how results are exported as Research Object bundles, including the PROV-O provenance of the workflow run. This is the original PPTX version (PowerPoint 2013), for PDF version see http://www.slideshare.net/soilandreyes/20130529-taverna-provenance
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2013-05-29 Taverna Provenance (pptx source)
- 1. TAVERNA PROVENANCE Stian Soiland-Reyes, University of Manchester https://github.com/wf4ever/taverna-prov This work is licensed under a Creative Commons Attribution 3.0 Unported License 2013-05-29
- 2. ARCHITECTURE Provenance Workflow Workflow run Process run (iteration) Parameter bindings Data Lists Values References Errors Process1 portA B C D E Process2 portA B C D E Invoke Retry Failover Loop Error bounce Provenance Parallelise Processor dispatch stack layer injected by plugin P Missier, S Soiland-Reyes, S Owen, W Tan, A Nenadic, I Dunlop, C Goble: (2010, January). Taverna, reloaded. In Scientific and Statistical Database Management (pp. 471-481). Springer Berlin Heidelberg. DOI 10.1007/978-3-642-13818-8_33 captures provenance trace Workflow execution
- 3. ONTOLOGY STACK tavernaprov • Lists, errors, byte content, checksums wfprov + wfdesc • Workflow execution, parameters, processes PROV-O • Activity start/stop, generation of values http://purl.org/wf4ever/wfprov# http://www.w3.org/ns/prov-o# http://ns.taverna.org.uk/2012/tavernaprov/
- 4. INTERMEDIATE RESULTS • Within the Taverna Workbench, the provenance database is used for showing intermediate results and previous runs Clicking a processor Inputs and outputs of individual invocations
- 5. WORKFLOW RESULTS (FOLDER) workflowrun.prov.ttl (RDF) outputA.txt outputC.jpg outputB/ Folder structure intermediates/ 1.txt 2.txt 3.txt de/def2e58b-50e2-4949-9980-fd310166621a.txt Workflow outputs, one file per value Provenance trace Values from intermediate steps in workflow
- 6. WORKFLOW RESULTS (BUNDLE) workflowrun.prov.ttl (RDF) outputA.txt outputC.jpg outputB/ https://w3id.org/bundle intermediates/ 1.txt 2.txt 3.txt de/def2e58b-50e2-4949-9980-fd310166621a.txt .ro/manifest.json inputA.txt workflow URI references attribution execution environment Aggregating in Research Object ZIP folder structure (RO Bundle) mimetype application/vnd.wf4ever.robundle+zip
- 7. ACKNOWLEDGEMENTS • Paolo Missier – initial provenance engine for Taverna 2 • Ian Dunlop – provenance capture execution layer • Khalid Belhajjame – ontologies • Alexandra Nenadic – intermediates, folder structure • W3C Provenance working group – PROV-O • Funded by European Commission’s 7th FWP FP7-ICT-2007-6 270192 and ESPRC platform grant EP/G026238/1
- 8. QUESTIONS? Twitter: @soilandreyes Skype: soiland Email: support@mygrid.org.uk http://soiland-reyes.com/stian/work/ http://practicalprovenance.wordpress.com/
Editor's Notes
- * Provenance is captured in Taverna by plugging into the execution stack of processors (See Taverna, Reloaded)* While running, data values and provenance traces are stored in internal database. * Provenance is captured for workflow run (including a copy of the workflow definition), process iterations (start/stop) and parameter input/output bindings to value references.
- PROV-O: Standard W3C ontology for provenance - we use it directly to record activity start/stop and generation of valueswfprov: An extension of PROV-O for tracking workflow execution, parameter bindings and subprocesses. Relates execution to an higher-level view of workflow structure (wfdesc)tavernaprov: An extension of wfprov for tracking Taverna-specific features, such as lists, error documents, and embed (not-so-large) byte content in RDF
- Within the Taverna Workbench, the internal provenance database is consulted to look up intermediate input/output values (individual processor invocations). This is used for debugging and verification. Workflow runs within the workbench can also be loaded up from the database at a later stage.
- Saving workflow results to a folder structureGenerates a file per value in the workflow outputs, named after portsNested folders for list outputs.Provenance trace (in RDF according using the ontology stack) relates output files to execution, links to intermediate values. (Values between processors who did not make it to an output port).
- The structure is similar to the folder, but is now inside a ZIP file. Augments the previous structure by also including the workflow definition, the inputs used for execution, a description of the execution environment, external URI references (such as the project homepage) and attribution to scientists who contributed to the bundle. This effectively forms a Research Object, all tied together by the RO Bundle Manifest, which is in JSON-LD format. (normal JSON that is also valid RDF).