M717report

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Contents

M7.17 Review of pilot mark up processes within the Scratchpad infrastructure

Due
23 November 2012
Delivered
21 November 2012
Purpose
To enable users to mark up text to add semantic information to the existing content.
Benefit
To mobilise the data in the literature through adding semantic metadata, resulting in a researcher being able to search and re-use the content more easily, as well as enabling automated re-use of the content by software tools.

Summary

The full GoldenGATE workflow was demonstrated and reviewed several times during the three days of workshops. This was a useful exercise for it confirmed that all GoldenGATE components were working as web services. As noted in [M716report M7.16] this is a monolithic workflow. The slow process of working through the full GoldenGATE workflow confirmed the correctness of the decision to extract components from GoldenGATE for individual use in M716. During the workshops we were able to explore the use of these components as individual web services and were able to confirm that:

  • they worked
  • no formal workflow could be established as each user will extract different semantic metadata, therefore the flexibility of our design is crucial to the success of the uptake of these individual web services.

Use

Owing to the amount of processing time a GoldenGATE web service may require (this is a result of the nature of the metadata extraction task, not a problem with the tool itself) the web srevices are not called directly from within Scratchpads. Instead, the services are enabled through the Oxford Batch Operation Engine OBOE in conjunction with Work Package 5.

Full integration will be achieved through OBOE's links to Scratchpads. The details of this work was discussed and agreed at the first of the workshops (see http://vbrant.eu/content/notes-oxford-workshop-21-november-2012).

For the purposes of the pilot review, we used GoldenGATE web services directly (as in M716) as well as through OBOE, to confirm both workflows. To use OBOE, the preferred long-term solution for integration into the Scratchpads infrastructure, in our pilot review, we navigated first to the OBOE home page and selected GoldenGATE services as shown below.

Screenshot showing OBOE's front page with GoldenGATE highlighted

Screenshot showing OBOE's front page with GoldenGATE highlighted

After signing in to the system, the various GoldenGATE web services are available to the user. A dynamic web form, the fields can vary depending on the job requested, is displayed allowing the user to upload a file for processing and set any optional parameters. Then the job is submitted and the user can track its progress as shown below.

Screenshot showing the interim status report from OBOE while a GoldenGATE job is running

Screenshot showing the interim status report from OBOE while a GoldenGATE job is running

In this example the GoldenGATE web service to identify date information within a text is being run. On completion the results are presented to the user as shown below.

Screenshot showing the results from OBOE having run a GoldenGATE job

Screenshot showing the results from OBOE having run a GoldenGATE job

The results are returned as inline XML mark up.

Conclusion

This marked up file is available for the users immediate use and for further automation mobilising the data content through whatever tools the user already has or could have developed that exploit this metadata now it can be extracted.

Workpackages
EMonocot
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