1. Wf4Ever: Annotating research objects Stian Soiland-Reyes, Sean Bechhofer myGrid, University of Manchester Open Annotation Rollout, Manchester, 2013-06-24 This work is licensed under a Creative Commons Attribution 3.0 Unported License 1

2. Motivation: Scientific workflows Coordinated execution of services and linked resources Dataflow between services Web services (SOAP, REST) Command line tools Scripts User interactions Components (nested workflows) Method becomes: Documented visually Shareable as single definition Reusable with new inputs Repurposable other services Reproducible? http://www.myexperiment.org/workflows/3355 http://www.taverna.org.uk/ http://www.biovel.eu/ 2

3. But workflows are complex machines Outputs Inputs Configuration Components http://www.myexperiment.org/workflows/3355 Will it still work after a year? 10 years? Expanding components, we see a workflow involves a series of specific tools and services which Depend on datasets, software libraries, other tools Are often poorly described or understood Over time evolve, change, break or are replaced User interactions are not reproducible But can be tracked and replayed 3

4. Electronic Paper Not Enough HypothesisExperiment Result Analysis Conclusions Investigation Data Electronic paper Publish http://www.force11.org/beyondthepdf2 http://figshare.com/ Open Research movement: Openly share the data of your experiments 4 http://datadryad.org/

5. http://www.researchobject.org/ RESEARCH OBJECT (RO) http://www.researchobject.org/ Research objects goal: Openly share everything about your experiments, including how those things are related 5

6. What is in a research object? A Research Object bundles and relates digital resources of a scientific experiment or investigation: Data used and results produced in experimental study Methods employed to produce and analyse that data Provenance and settings for the experiments People involved in the investigation Annotations about these resources, that are essential to the understanding and interpretation of the scientific outcomes captured by a research object http://www.researchobject.org/ 6

7. Gathering everything Research Objects (RO) aggregate related resources, their provenance and annotations Conveys “everything you need to know” about a study/experiment/analysis/dataset/workflow Shareable, evolvable, contributable, citable ROs have their own provenance and lifecycles 7

8. Why Research Objects? i.To share your research materials (RO as a social object) ii.To facilitate reproducibility and reuse of methods iii.To be recognized and cited (even for constituent resources) iv.To preserve results and prevent decay (curation of workflow definition; using provenance for partial rerun) 8

9. A Research object http://alpha.myexperiment.org/packs/387 9

10. 10

11. Quality Assessment of a research object 11

12. Quality Monitoring 12

13. Annotations in research objects Types: “This document contains an hypothesis” Relations: “These datasets are consumed by that tool” Provenance: “These results came from this workflow run” Descriptions: “Purpose of this step is to filter out invalid data” Comments: “This method looks useful, but how do I install it?” Examples: “This is how you could use it” 13

14. Annotation guidelines – which properties? Descriptions: dct:title, dct:description, rdfs:comment, dct:publisher, dct:license, dct:subject Provenance: dct:created, dct:creator, dct:modified, pav:providedBy, pav:authoredBy, pav:contributedBy, roevo:wasArchivedBy, pav:createdAt Provenance relations: prov:wasDerivedFrom, prov:wasRevisionOf, wfprov:usedInput, wfprov:wasOutputFrom Social networking: oa:Tag, mediaont:hasRating, roterms:technicalContact, cito:isDocumentedBy, cito:isCitedBy Dependencies: dcterms:requires, roterms:requiresHardware, roterms:requiresSoftware, roterms:requiresDataset Typing: wfdesc:Workflow, wf4ever:Script, roterms:Hypothesis, roterms:Results, dct:BibliographicResource 14

15. What is provenance? By Dr Stephen Dann licensed under Creative Commons Attribution-ShareAlike 2.0 Generic http://www.flickr.com/photos/stephendann/3375055368/Dr Stephen Dann http://www.flickr.com/photos/stephendann/3375055368/ Attribution who did it? Derivation how did it change? Activity what happens to it? Licensing can I use it? Attributes what is it? Origin where is it from? Annotations what do others say about it? 15 Aggregation what is it part of? Date and tool when was it made? using what?

16. Attribution Who collected this sample? Who helped? Which lab performed the sequencing? Who did the data analysis? Who curated the results? Who produced the raw data this analysis is based on? Who wrote the analysis workflow? Why do I need this? i.To be recognized for my work ii.Who should I give credits to? iii.Who should I complain to? iv.Can I trust them? v.Who should I make friends with? prov:wasAttributedTo prov:actedOnBehalfOf dct:creator dct:publisher pav:authoredBy pav:contributedBy pav:curatedBy pav:createdBy pav:importedBy pav:providedBy... Roles Person Organization SoftwareAgent Agent types Alice The lab Data wasAttributedTo actedOnBehalfOf 16 http://practicalprovenance.wordpress.com/

17. Derivation Which sample was this metagenome sequenced from? Which meta-genomes was this sequence extracted from? Which sequence was the basis for the results? What is the previous revision of the new results? Why do I need this? i.To verify consistency (did I use the correct sequence?) ii.To find the latest revision iii.To backtrack where a diversion appeared after a change iv.To credit work I depend on v.Auditing and defence for peer review wasDerivedFrom wasQuotedFrom Sequenc e New results wasDerivedFrom Sample Meta - genome Old results wasRevisionOf wasInfluencedBy 17

18. Activities What happened? When? Who? What was used and generated? Why was this workflow started? Which workflow ran? Where? Why do I need this? i.To see which analysis was performed ii.To find out who did what iii.What was the metagenome used for? iv.To understand the whole process “make me a Methods section” v.To track down inconsistencies used wasGeneratedBy wasStartedAt "2012-06-21" Metagenom e Sample wasAssociatedWith Workflow server wasInformedBy wasStartedBy Workflo w run wasGeneratedBy Results Sequencing wasAssociatedWith Alice hadPlan Workflow definition hadRole Lab technician Results 18

19. PROV model http://www.w3.org/TR/prov-primer/ Copyright © 2013 W3C® (MIT, ERCIM, Keio, Beihang), All Rights Reserved. Entity Agen t Activity wasDerivedFrom Provenance Working Group 19

20. Provenance of what? Who made the (content of) research object? Who maintains it? Who wrote this document? Who uploaded it? Which CSV was this Excel file imported from? Who wrote this description? When? How did we get it? What is the state of this RO? (Live or Published?) What did the research object look like before? (Revisions) – are there newer versions? Which research objects are derived from this RO? 20

21. Research object model at a glance 21 Researc h Object Resourc e Annotatio n oa:hasTarget Resource Annotation graph oa:hasBody ore:aggregates «ore:Aggregation» «ro:ResearchObject» «oa:Annotation» «ro:AggregatedAnnotation» «trig:Graph» «ore:AggregatedResource» «ro:Resource» Manifest «ore:ResourceMap» «ro:Manifest» ore:isDescribedBy

22. Wf4Ever architecture 22 Blob store Graph store Resourc e Uploaded to Manifest Annotation graph Resear ch object Annotation Redirects to ORE Proxy External referenc e Redirects to If RDF, import as named graph SPARQ L queries REST resources http://www.wf4ever- project.org/wiki/display/docs/RO+API+6

23. Where do RO annotations come from? Imported from uploaded resources, e.g. embedded in workflow-specific format (creator: unknown!) Created by users filling in Title, Description etc. on website By automatically invoked software agents, e.g.: A workflow transformation service extracts the workflow structure as RDF from the native workflow format Provenance trace from a workflow run, which describes the origin of aggregated output files in the research object 23

24. How we are using the OA model Multiple oa:Annotation contained within the manifest RDF and aggregated by the RO. Provenance (PAV, PROV) on oa:Annotation (who made the link) and body resource (who stated it) Typically a single oa:hasTarget, either the RO or an aggregated resource. oa:hasBody to a trig:Graph resource (read: RDF file) with the “actual” annotation as RDF: dct:title "The wonderful workflow". Multiple oa:hasTarget for relationships, e.g. graph body: roterms:inputSelected. 24

25. What should we also be using? Motivations myExperiment: commenting, describing, moderating, questioning, replying, tagging – made our own vocabulary as OA did not exist Selectors on compound resources E.g. description on processors within a workflow in a workflow definition. How do you find this if you only know the workflow definition file? Currently: Annotations on separate URIs for each component, described in workflow structure graph, which is body of annotation targeting the workflow definition file Importing/referring to annotations from other OA systems (how to discover those?) 25

26. What is the benefit of OA for us? Existing vocabulary – no need for our project to try to specify and agree on our own way of tracking annotations. Potential interoperability with third-party annotation tools E.g. We want to annotate a figure in a paper and relate it to a dataset in a research object – don’t want to write another tool for that! Existing annotations (pre research object) in Taverna and myExperiment map easily to OA model 26

27. History lesson (AO/OAC/OA) When forming the Wf4Ever Research Object model, we found: Open Annotation Collaboration (OAC) Annotation Ontology (AO) What was the difference? Technically, for Wf4Ever’s purposes: They are equivalent Political choice: AO – supported by Utopia (Manchester) We encouraged the formation of W3C Open Annotation Community Group and a joint model Next: Research Object model v0.2 and RO Bundle will use the OA model – since we only used 2 properties, mapping is 1:1 27 http://www.wf4ever-project.org/wiki/display/docs/2011-09-26+Annotation+model+considerations

28. Saving a research object: RO bundle Single, transferrable research object Self-contained snapshot Which files in ZIP, which are URIs? (Up to user/application) Regular ZIP file, explored and unpacked with standard tools JSON manifest is programmatically accessible without RDF understanding Works offline and in desktop applications – no REST API access required Basis for RO-enabled file formats, e.g. Taverna run bundle Exchanged with myExperiment and RO tools

29. 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 inputA.txt workflow URI reference s attribution execution environment Aggregating in Research Object ZIP folder structure (RO Bundle) mimetype application/vnd.wf4ever.robundle+zip.ro/manifest.jso n

30. RO Bundle What is aggregated? File In ZIP or external URI Who made the RO? When? Who? External URIs placed in folders Embedded annotation External annotation, e.g. blogpost JSON-LD context  RDF RO provenance.ro/manifest.json Format Note: JSON "quotes" not shown above for brevity http://json-ld.org/ http://orcid.org/ https://w3id.org/bundle

31. 31 http://mayor2.dia.fi.upm.es/oeg-upm/files/dgarijo/motifAnalysisSite/ Common Motifs in Scientific Workflows: An Empirical Analysis <body resource="http://www.oeg-upm.net/files/dgarijo/motifAnalysisSite/" typeOf="ore:Aggregation ro:ResearchObject"> Research Object as RDFa http://www.oeg-upm.net/files/dgarijo/motifAnalysisSite/ <a property="ore:aggregates" href="t2_workflow_set_eSci2012.v.0.9_FGCS.xls" typeOf="ro:Resource">Analytics for Taverna workflows <a property="ore:aggregates" href="WfCatalogue-AdditionalWingsDomains.xlsx“ typeOf="ro:Resource">Analytics for Wings workflows <span property="dc:creator prov:wasAttributedTo" resource="http://delicias.dia.fi.upm.es/members/DGarijo/#me">

32. W3C community group for RO http://www.w3.org/community/rosc/ 32