My work at ISI during the summer, its relation with wf4Ever and next steps in my research

1. Work at ISI, relationwith wf4Ever,futuresteps Daniel GarijoVerdejo,Yolanda Gil Ontology Engineering Group. Laboratorio de Inteligencia Artificial Departamento de Inteligencia Artificial Facultad de Informática Universidad Politécnica de Madrid Date: 13/10/2011

2. The TB Drugome 1

3. Project goals Typical Published Article Reproducible Article: Weaver, GenePattern GRRD, etc. Text: Narrative of method, software packages used Text: Narrative of method, software packages used Data: Key datasets and figures/plots Data: Key datasets and figures/plots Workflow: Workflow/scripts describing dataflow, codes, and parameters NOT published, loosely recorded: Software: scripted codes + manual steps + notes/emails 3

5. Eg: eHits was proprietary and replaced by AutodockVina

6. Different labs prefer different codes

7. Eg: R vsMatlab

10. Description of workflow that is independent of the codes executed

11. Maps to the codes executed (the “executable workflow”)

12. Publish both abstract and executable workflow using the OPM standard

13. OPM (Open Provenance Model) is independent of workflow framework and is widely implemented

14. Other groups can import to their own workflow framework

15. Publish data and workflows as Linked Data on the Web

16. All workflows and related files are web-accessible

17. Simple mechanism to share across local file systems5

18. High level architecture Other workflow environments WINGS on local laptop Workflow Template Core OPMexport Programatic access(external apps) Portal WorkflowInstance LinkedDataPublication WINGS on shared host Workflow Template Core OPMexport Portal WorkflowInstance Interactive Browsing(Pubby frontend) WINGS on web server Workflow Template Core OPMexport Users Portal WorkflowInstance Wings workflow generation OPMconversion Publication Share Reuse 6

19. High level architecture (2) Linked Data publication Abstract Workflow (OPM) RDF Upload Interface Wings OPMexport ExecutableWorkflow (OPM) Other workflow frameworks RDF Triple store OPMimport Permanentweb-accessible filestore SPARQL Endpoint Web accessible Workflow Data, Components, etc. ISI web servers (http://wings.isi.edu/…) Amazon EC2 cloud (http://ec2-184-72-160-64.…) Web browser Needed if workflow was developed in local host instead of a public server 7

20. Executable and abstract workflow 8

21. hasArtifactTemplate Artifact account Artifact Artifact Artifact Input artifact1 Input artifact2 Execution Input1 Execution Input2 hasArtifactTemplate user account used used used hasArtifact account wasControlledBy Process used Agent Execution account Workflowtemplate Abstract template Node Execution Node account hasProcessTemplate hasProcess hasAbstractComponent Process hasSpecificComponent Account OPM Graph wasGeneratedBy subClassOf hasArtifact Abstractcomponent Specificcomponent account wasGeneratedBy Outputartifact1 Execution result hasArtifactTemplate Artifact Artifact hasWorkflowTemplate Workflow Template Execution Results OPMV extended model Red: OPM model Black: OPM profile (extension) 9

23. Reproducibility by an expert

24. Basic reproducibility by non-experts

25. Reproducibility by students from text only

26. Or, not reproducible at all10

27. Reproducibility Maps Comparison of ligand binding sites using SMAP Comparison of dissimilar protein structures using FATCAT Docking using eHits/AutodockVina 11

28. Reproducibility maps: accessing the scripts and intermediate data 12

30. Complement to the workflow, to understand it better.

31. Allows tackling incomplete provenance.

32. Additional workflow repository for recommendation

33. OPM (Open Provenance Model) is independent of workflow framework and is widely implemented (Taverna has a OPM export too)

34. Other groups can import to their own workflow framework

35. Workflow integration with WINGS.

36. Semantic annotation of workflows.

37. Distributed workflow execution engine13

39. Research on compatibility with problem solving methods (PSMs).

40. Create an OPMV/W3C PROV-O profile for common workflow representation.

41. Interoperability between workflow systems (Taverna).

42. Work in workflows in different domains.

43. Biology, Astronomy.

44. Workflow reuse between different domains?14

46. OPMO + OPMV mapped version: http://openprovenance.org/model/opmo

47. WINGS workflow system: http://seagull.isi.edu/marbles/

48. TB Drugome Wiki (Evolution of the work): http://seagull.isi.edu/wings-drugome/index.php/Main_Page

49. Thanks to Yolanda Gil for letting me borrowing some of the Slides based on USCD slides for this presentation.15

50. Work at ISI, relationwith wf4Ever,futuresteps Daniel GarijoVerdejo Ontology Engineering Group. Laboratorio de Inteligencia Artificial Departamento de Inteligencia Artificial Facultad de Informática Universidad Politécnica de Madrid Date: 03/10/2011