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A user view on provenance of ROs and their content.

The tables below are copied from UserViewOfProvenance.ods (as pdf: UserViewOfProvenance.pdf). They are in DropBox here.

The current state (29/2/2012) is draft.

User view 1

 



Comments

In general, avoid the term provenance towards users. Embed it in something else. Make purpose the focus.
(e.g. Taverna allowing us to save a 'workflow run', rather than 'export provenance').

 

 

 

 

 

Imo we cannot enforce much about the provenance of external sources; guidelines should state that it should be there, but in which form should follow domain best practices (our tools should be flexible for that)

 

 

 

 

 

I have not investigate ISA-TAB and followers in detail. Perhaps this can be used here.

 

 

RO type

User Roles

When I click on

I would like to see

User priority
(1: lowest - 5: highest)

uvp1.1

Live RO

Researcher

A workflow

Previous runs, when they were run, who ran them, summary of results and comments on the run

 

uvp1.2

Snapshot RO

Supervisor

A workflow

Idem, + why they were run, comments require an interpretation of results of run

 

uvp1.3

Published RO

Reader, Reviewer

A workflow

1. Runs of this workflow, when they were run, why they were saved, what results they produced, who ran them, comments for reviewer/readers

 

uvp1.4

 

 

 

2. Published ROs that used this workflow in some way, run status of the workflows in there, type of results, who, when

 

uvp1.5

Live RO

Researcher

A workflow result

Workflow and Workflow run that produced it, who ran it, when, comments on that run

 

uvp1.6

Snapshot RO

Supervisor

A workflow result

Idem, + why they were run, comments require an interpretation of results

 

uvp1.7

Published RO

Reader, Reviewer

A workflow result

1. Workflow and Workflow run that produced it, who ran it, when, comments for reviewers/readers

 

uvp1.8

 

 

 

2. Workflows/ROs that used these results in some way, when and who

 

uvp1.9

Live RO

Researcher

A workflow input

Source of input (sometimes), who and what produced it, when [via a reference or annotation]; runs it was used in

 

uvp1.10

Snapshot RO

Supervisor

A workflow input

Source of input, what it represents, who and what produced it, why it was used, runs it was used for (if any), comments on input

 

uvp1.11

Published RO

Reader, Reviewer

A workflow input

Source of input, what it represents, who and what produced it, why it was used, runs it was used for, comments for reader/reviewer

 

uvp1.12

Live RO

Researcher

A workflow run

1. Overview: Workflow it was a run of, who ran it, when, its results, comments on the run

 

uvp1.13

 

 

 

2. Deeper view: report on dependencies*, where it went wrong, detailed comments

 

uvp1.14

Snapshot RO

Supervisor

A workflow run

Workflow it was a run of, the purpose of that workflow, who ran it, when, why, its results, interpretation of the results, comments on the run

 

uvp1.15

Published RO

Reader, Reviewer

A workflow run

Workflow it was a run of, the purpose of that workflow, who ran it, when, why, its results, comments for reader/reviewer

 

uvp1.16

Live RO

Researcher

Live RO

What external materials were used (including content from other ROs), critical dependencies, preferred: + who made them and when, their comments for readers

 

uvp1.17

Snapshot RO

Supervisor

Snapshot RO

Idem, + why they were used, + who/what made them (acknowledgement), critical dependencies, runs of workflows in the RO (if any), comments on the RO

 

uvp1.18

Published RO

Reader, Reviewer

Published RO

What external materials were used (references and acknowledgements), critical dependencies, comments for reader/reviewer

 

* Dependencies not necessarily as in coding; could also be the availability of a dataset, or even something we cannot imagine yet => requires human annotation

User view 2

This is how I started, it turned out to not be trivial to decide on what to do sometimes.

 

I click on

... and see these fields

 

 

 

 

 

 

 

 

What happened?

When?

By whom?

By What?

Why?

before

after

uvp2.1

Workflow run xxx

Interpreted GWAS data by text mining

12/12/11

Kristina Hettne

Taverna version vvv

Discover biological concepts involved in Metabolic Syndrome

Collected GWAS data

Interpreted workflow results

uvp2.2

Workflow input of run xxx= GWAS dataset

Instantiated workflow with input

12/12/11

 

Taverna version vvv

Discover biological concepts involved in Metabolic Syndrome

Collected GWAS data

Instantiated workflow

uvp2.3

Workflow output

Produced workflow result

12/12/11

 

Taverna version vvv

 

Ran workflow xxx

Interpreted workflow results

uvp2.4

Published Research Object rrr

Published RO

22/12/11

Kristina Hettne

 

Publish GWAS interpretation results

Submitted RO

 

uvp2.5

Web service run yyy

Produced concepts related to gene set

12/12/11

 

Taverna version vvv

Discover biological concepts associated with input concepts

Produced genes

Selected first 10

uvp2.6

service input

Provided input

10/12/11

Harish Dharuri

 

Input to workflow xxx in RO rrr

Ran workflow yyy

Ran workflow xxx

uvp2.7

service output

Provided output

12/12/11

 

Workflow xxx

Suggest biological concepts involved in Metabolic Syndrome

Ran workflow xxx

Interpreted workflow results

uvp2.8

GWAS data

Collected GWAS data

11/12/11

Peter Henneman

Manually

Provide input

GWAS of a
Dutch population

ran workflow xxx

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