Scientific data management from the lab to the web

Editor's Notes

• #10: In this scenario student Dennis has made a conceptual workflow that takes the result of a gene expression experiment (activity values of all genes under two conditions: with/without a chemical compound). The wet laboratory experiment was done by others then Dennis. He makes a note of the origin (including a paper reference). The initial hypothesis is that the chemical compound disturbs gene expression. It is yet unknown which genes and what biological processes are affected. The conceptual workflow first performs one of the standard data preprocessing steps for the type of data Dennis has (Affymetrix gene expression array), then it uses a statistical test to filter those genes that are significantly differentially expressed between the two conditions, and finally it performs an enrichment test to find those pathways that are most prominent among the filtered genes. The latter requires an annotation process, where each gene is coupled to the pathways it was once implied in in other experiments (there is a database for that: KEGG).Dennis is new to workflows, so he wishes to start with an existing workflow. For each component he will search myExperiment for keywords. He then wishes to understand the workflows: look into them, perform test runs with test data and his own data, and see other peoples logs. When he finds workflows he does not understand, Dennis is inclined to create his own workflow with his own scripts. He will receive scripts from colleagues and perform tests that his colleagues are familiar with. As such, he can learn what his workflow is doing. This will help him interpret his results.Ultimately, the workflow may suggest for instance that the set of differentially expressed genes has the Wnt pathway as most common denominator. This pathway is well known for embryogenesis and cancer, information he finds on the internet. He makes a note of that. It will lead to the hypothesis that the chemical compound, may have effects on embryogenesis and/or cancer. This is now his interpretation of his experiment that he wishes to link to his experiment and the processed data. Dennis notes that in a next cycle he will want to perform another workflow that specifically tests this hypothesis, rather that perform an enrichment test. He will then look for a workflow that performs a 'global test', and replace this part in his workflow with the global test workflow. In his log he indicates this fact. In this case he will link the result of this test (most likely a new hypothesis) to the previous experiment and in particular to the initial hypothesis. At some point, he wishes to be able to retrieve this past information and the interrelationships among his hypotheses.Assuming his finding and new hypothesis are valuable and new, he will publish his results. The publication has cleaned information, sufficient for evaluating his hypothesis and rerunning the one workflow and the one dataset that lead to this result.Dennis Working Research Object will containA reference to the source of the data and the people to acknowledge for it.The initial hypothesisThe conceptual workflow or a summary of the experiment planReferences to workflows that were tested, with comments on their application for Dennis caseA reference to the workflow(s) that Dennis eventually uses, including acknowledgement information (including a note on how these people want to be acknowledged)Dennis his workflow, possibly with a backlog of previous versions that Dennis wishes to keep for reference (with notes and comments)Dennis his workflow run, results and the recorded steps that lead to the results, in some cases with comments for later reference (e.g. 'here I used parameter A, next time I may try B')The final hypothesis, with comments.A reference to the results of the workflowA Design log that records Dennis considerations while making the workflowA Run log that records Dennis considerations while running and interpreting the workflowHis Publication Research Object will containThe workflowA caption for his workflow (filtered from his design and run log, all information necessary to run the experiment by a reviewer)A workflow run (results, and a caption filtered from run log)His initial hypothesisHis final hypothesisThe data sourceAcknowledgementsIn time, Dennis' workflow can be found on the basis of his Published and Working RO's metadata. This will create a rich and wide range of search capabilities for Dennis' successors.The Working RO is kept at Dennis local group, and is the most valuable resource for reusing the work. The Published RO is available for download and reuse. It is anticipated that interested parties will contact Dennis or his group for 'reuse in collaboration' (i.e. for the group's expertise).
• #11: Emphasise the use of Linked Data. Note: the figures here are not intended to be readable. They’re simply emphasising the existence of the models. Example user requirements being addressed by RO:UR1.3 aggregate existing resources to conveniently access related resources from a single placeUR1.6 describe the relationships between aggregated resources so that other researchers can see how the resources fit togetherUR1.16 annotate experimental results using semantic models so that I can find/show links to other, relevant research objects