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SHARP: harmonizing Galaxy and Taverna worflow provenance

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The slides of the demo given at SeWeBMeDDA workshop (https://sites.google.com/insight-centre.org/sewebmeda/home) co-located with ESWC 2017.

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SHARP: harmonizing Galaxy and Taverna worflow provenance

  1. 1. SHARP: Harmonizing Galaxy and Taverna workflow provenance SeWeBMeDA’17 - Demonstration Alban Gaignard1 , Khalid Belhajjame2 , Hala Skaf-Molli3 May 28, 2017 1 Nantes Academic Hospital, France 2 LAMSADE Paris-Dauphine University, France 3 LS2N - Nantes University, France
  2. 2. Multiple workflow engines Taverna workflow @research-lab Galaxy workflow @sequencing-facility Variant effect prediction VCF file Exon filtering output Merge Alignment sample 1.a.R1 sample 1.a.R2 Alignment sample 1.b.R1 sample 1.b.R2 Alignment sample 2.R1 sample 2.R2 Sort Sort Variant calling GRCh37 go to owl:sameAs A. Gaignard, K. Belhajjame, H. Skaff Molli – SeWeBMeDA’17 1
  3. 3. SHARP approach owl:sameAs inferred PROV PROV trace PROV trace nanopub PROV interlinking PROV harmonization PROV summarization 11 12 13 … 14 A. Gaignard, K. Belhajjame, H. Skaff Molli – SeWeBMeDA’17 5
  4. 4. Demonstration scenario – Provenance capture — Provenance interlinking ˜ Provenance harmonization ™ Provenance summarization (influence graphs, nanopublications) • https://github.com/albangaignard/galaxy-PROV • https://github.com/albangaignard/sharp-prov-toolbox A. Gaignard, K. Belhajjame, H. Skaff Molli – SeWeBMeDA’17 6
  5. 5. – Provenance capture Taverna Built-in when saving workflow execution results. Galaxy GALAXY-PROV tool + web interface: • API key • list Galaxy data processing histories • generate PROV (turtle) • visualize PROV (D3.js) https://github.com/albangaignard/galaxy-PROV A. Gaignard, K. Belhajjame, H. Skaff Molli – SeWeBMeDA’17 7
  6. 6. Galaxy workflow provenance capture demo A. Gaignard, K. Belhajjame, H. Skaff Molli – SeWeBMeDA’17 7
  7. 7. — Provenance interlinking 1. SHA-512 fingerprint of files 2. annotating PROV entities with SHA-512 digest 3. producing owl:sameAs → SPARQL CONSTRUCT-WHERE query Command line tool java -jar SharpProvToolbox/target/SHARP-1.0-SNAPSHOT-launcher.jar -ri sample-data/control_mm9_chr15_Plekhh2-PigF_forward.fastq sample-data/control_mm9_chr15_Plekhh2-PigF_reverse.fastq sample-data/drugged_mm9_chr15_Plekhh2-PigF_forward.fastq sample-data/drugged_mm9_chr15_Plekhh2-PigF_reverse.fastq sample-data/unknown.fastq A. Gaignard, K. Belhajjame, H. Skaff Molli – SeWeBMeDA’17 10
  8. 8. ˜ Provenance harmonization 1. OWL entailments, Jena API ReasonerRegistry.getOWLMiniReasoner() 2. PROV inferences (TGD), Jena rule engine new GenericRuleReasoner(all prov rules) 3. Blank nodes removing (EGD) Command line tool java -jar SharpProvToolbox/target/SHARP-1.0-SNAPSHOT-launcher.jar -i sample-data/taverna.prov.ttl sample-data/galaxy.prov.ttl sample-data/sameas.ttl A. Gaignard, K. Belhajjame, H. Skaff Molli – SeWeBMeDA’17 12
  9. 9. ™ Provenance summarization: influence graph CONSTRUCT { ?x ?p ?y . ?x rdfs:label ?lx . ?y rdfs:label ?ly . } WHERE { ?x ?p ?y . FILTER (?p IN (prov:wasInfluencedBy)) . ?x rdfs:label ?lx . ?y rdfs:label ?ly . } + HTML/D3.js code generation Command line tool java -jar SharpProvToolbox/target/SHARP-1.0-SNAPSHOT-launcher.jar -i sample-data/taverna.prov.ttl sample-data/galaxy.prov.ttl sample-data/sameas.ttl -s A. Gaignard, K. Belhajjame, H. Skaff Molli – SeWeBMeDA’17 14
  10. 10. ™ Provenance summarization: nanopublication CONSTRUCT { GRAPH :assertion { ?ref_genome a sio:Genome . ?sample a sio:Sample ; sio:is-variant-of ?ref_genome ; sio:has-phenotype ?out . [...] } } WHERE { [...] ?out ( prov:wasInfluencedBy )+ ?sample . [...] } Command line tool java -jar SharpProvToolbox/target/SHARP-1.0-SNAPSHOT-launcher.jar -i sample-data/taverna.prov.ttl sample-data/galaxy.prov.ttl sample-data/sameas.ttl -sq sample-data/nanopub.query A. Gaignard, K. Belhajjame, H. Skaff Molli – SeWeBMeDA’17 16
  11. 11. Questions ? alban.gaignard@univ-nantes.fr Acknowledgments
  12. 12. Backup slides A. Gaignard, K. Belhajjame, H. Skaff Molli – SeWeBMeDA’17 19
  13. 13. PROV-O ontology https://www.w3.org/TR/prov-o A. Gaignard, K. Belhajjame, H. Skaff Molli – SeWeBMeDA’17 20

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