2013-07-19 myExperiment research objects, beyond workflows and packs (PPTX)

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Presentation at BOSC 2013 / ISMB 2013. (PowerPoint 2013 source)

PDF: https://www.slideshare.net/soilandreyes/2013-0719bosc-2013myexperimentresearchobjectsslides

See also poster at http://www.slideshare.net/soilandreyes/2013-0718bosc-2013myexperimentresearchobjectsposter-24242509 or
submitted abstract: https://docs.google.com/document/d/1jaAuPV-EnbsyI14L56HKHBQP7eDVfeXGLlK-LwohnWw/edit?usp=sharing


We have evolved Research Objects as a mechanism to preserve digital resources related to research, by providing mechanisms, formats and architecture for describing aggregated resources (hypothesis, workflow, datasets, scripts, services), their relations (is input for, explains, used by), provenance (graph was derived from dataset A, B and C) and attribution (who contributed what, and when?).

The website myExperiment is already popular for collaborating on, publishing and sharing scientific workflows, however we have found that for understanding and preserving a workflow over time, its definition is not enough, specially faced with workflow decay, services and tools that change over time. We have therefore adapted the research object model as a foundation for the myExperiment packs, allowing uploading of workflow runs, inputs, outputs and other files relevant to the workflow, relating them with annotations and integrated the Wf4Ever architecture for performing decay analysis and tracking a research object’s evolution as it and its constituent resources change over time.

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  • http://purl.org/wf4ever/model
  • http://purl.org/wf4ever/model
  • Typing of resources and relating them to each-other are individual annotations
  • Quality metrics are monitored over time, so as the research object evolves (say gaining additional annotations), the health of the annotations can be indicated graphically.
  • Sequencing machines:illumina
  • W3C standardisation body HTML
  • So for Wf4Ever, what kind of provenance are we talking about? It is a bit more down to earth as we are generally just talking about files and documents, but still, as you form a research object combining many different resources, the different dimensions of provenance become increasingly important to track.
  • So let’s have a look at what a Research Object looks like. The core is the concept of the Research Object itself, which you may also known as an ORE aggregation. This is described by the manifest, which is simply an RDF file. The RO aggregates a series of resources – in Linked Data these could be anywhere in the world. Additionally it aggregates a set of annotations, which we know is the link between a target resource (here aggregated in the RO), and an body resource. In Wf4Ever we typically provide the body as a separate RDF Graph, so that we can use existing vocabularies to describe and relate the resources.
  • So not everyone have access to set up a RESTful semantic web servers, in particular we’ve run into this with desktop applications – users just want to save files and then they decide where they are stored. So we decided to write a serialization format for Research Object, which we call the RO Bundle.We wanted this to be accessible for applicaton developers, so we’ve adopted ZIP and JSON, and in a way this would let you create research objects and make annotations without ever seing any RDF.
  • This shows how the JSON manifest focuses on the most common aspect of a research object – who made it? When? What is aggregated – files in the ZIP but also external URIs – up to the application or person making the bundle to decide what is to be included in the ZIP. Annotations are included at the bottom here, we see that there’s an annotation “about” (target) the analysis JPEG, and the content (the body) is within the annotations/ folder. Similarly, the next annotations relates the external resource (a blog post) with our aggregation of a resource.This is processable as JSON-LD – so it is not just JSON, it is also RDF, and out comes normal ORE aggregations and OA annotations.
  • This is how we represent a workflow run as a Workflow Results RO Bundle. We aggregate the workflowoutputs, , 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).
  • So we have recently formed a W3C Community Group for Research Object, which has gathered significant interest, 75 participant. As you see, I am one of the chairs, and so is Rob which you already know from OA group. We are just starting up, and our focus in the RO community group is rather how to practically use Research Objects as a concept than to specify a new model – we’ll refer to existing models where it’s appropriate, but also explore other models which could be described as research objects.
  • 2013-07-19 myExperiment research objects, beyond workflows and packs (PPTX)

    1. 1. myExperiment Research Objects: Beyond Workflows and Packs Stian Soiland-Reyes myGrid, University of Manchester BOSC 2013, ISMB, Berlin, 2013-07-19 This work is licensed under a Creative Commons Attribution 3.0 Unported License
    2. 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/
    3. 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
    4. 4. Electronic Paper Not Enough Hypothesis Experiment Result Analysis Conclusions Investigation Data Data Electronic paper Publish http://www.force11.org/beyondthepdf2http://figshare.com/ Open Research movement: Openly share the data of your experiments http://datadryad.org/
    5. 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
    6. 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/
    7. 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
    8. 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)
    9. 9. A Research object http://alpha.myexperiment.org/packs/387
    10. 10. QualityAssessment of a research object
    11. 11. QualityMonitoring
    12. 12. 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. 13. What is provenance? By Dr Stephen Dann licensed under Creative Commons Attribution-ShareAlike 2.0 Generic 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? Abstraction levels shallots, sign, photo or flickr page? Aggregation what is it part of? Date and tool when was it made? using what?
    14. 14. Attribution Who collected this sample? Who helped? Which lab performed the sequencing? Who did the data analysis? Who wrote the analysis workflow? Who made the data set used by analysis? Who curated the results? 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? Alice The lab Data wasAttributedTo actedOnBehalfOf
    15. 15. 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 Sequence New results wasDerivedFrom Sample Meta - genome Old results wasRevisionOf wasInfluencedBy
    16. 16. 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" Metagenome Sample wasAssociatedWith Workflow server wasInformedBy wasStartedBy Workflow run wasGeneratedBy Results Sequencing wasAssociatedWith Alice hadPlan Workflow definition hadRole Lab technician Results
    17. 17. Core PROV model http://www.w3.org/TR/prov-primer/ Copyright © 2013 W3C® (MIT, ERCIM, Keio, Beihang), All Rights Reserved. Provenance Working Group
    18. 18. 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?
    19. 19. Research object model at a glance Research Object Resource Resource Resource Annotation Annotation Annotation oa:hasTarget Resource Resource Annotation graph oa:hasBody ore:aggregates Manifest
    20. 20. Wf4Ever architecture Semantic REST API RDF triple store (RO structure, Annotations) RO index Uploaded files PortalChecklist service Command line Workflow runner ...
    21. 21. 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
    22. 22. Example RO bundle: Workflow Results workflowrun.prov.ttl (RDF) outputA.txt outputC.jpg outputB/ https://w3id.org/bundl intermediates/ 1.txt 2.txt 3.txt de/def2e58b-50e2-4949-9980-fd310166621a.txt inputA.txt workflow URI references attribution execution environment Aggregating in Research Object ZIP folder structure (RO Bundle) mimetype application/vnd.wf4ever.robundle+zip .ro/manifest.json
    23. 23. W3C community group for RO http://www.w3.org/community/rosc/
    24. 24. Summary Provide provenance records: Use (and extend) PROV. Share your methods (tools, workflows), not just your data Make research objects: Collect resources and relate them Pick your RO integration level to adapt: 1. Conceptual model 2. RO Core ontology (aggregation and annotation) 3. Workflow description and provenance 4. Wf4Ever architecture for APIs 5. myExperiment as user interface

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