05.06.2014 BiolDiv

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Meeting Thursday 5 June 2014

Present: Fabio, GP, Nicolas (from the deep), Anton, Edward.




CRIA wants to step up its presence in iMarine. They have plenty of experience in creating tools for data quality control, and want to use this to contribute to iMarine. More specifically, it should be investigated how BiOnym can relate to these tools.

There have been some email exchanges between Vanderlei and Dora, and Nicolas and Edward. We need a three-way teleconference between CRIA, Nicolas and Edward to see how to take this further.

BiOnym Interface

  • There were regular new versions of the interface, latest at http://bionym.d4science.org:8080/bionym-portletv4/.
  • But this version does not function properly. It takes a very long time for anything to be returned (if at all), which makes experimenting very difficult. Most of the time, if there is a response, the list of possible matches is empty, sometimes there are several alternatives but not the one that is obviously the correct one.
  • GP has tried to contact Casey to discuss problems, but didn't receive a reply (it turned ou tthat Casey was on leave to attend familial issues).
  • Next week's meeting we will discuss further action; we hope that by then issues will have been resolved - both communications and the interface itself.
  • Anton wanted to make the link to the interface available in preparation for the board meeting. With the present state of the interface, we'll have to postpone.
  • Together with the link of the interface, we can make the link to BiOnym through the statistical manager available (https://i-marine.d4science.org/group/bionym/bionym-app). That would show one of the characteristics of developments in iMarine, where the same functionality is available through different windows, customised for different audiences. If the link through the statistical Manager is made available, we should also explain how to request permission to get access.


  • Seems we're nearing the end for the internal report version of the document. The paper seems to be stable now, and the sequence of the sections logical. Next steps:
    • GP is moving everything to LaTeX; the document is now 40 pages, so this will take a while (expected to be finished tomorrow (Friday) evening)
    • Fabio and Edward to provide 'supplementary material', by placing on [[1]] (=[[2]]):
      • R code for simulation of misspellings
      • R code for AUC Curves and triax diagrams
      • Datasets of the experiments
      • Datasets for parsers comparison
      • Datasets for results by parsers
    • Do not edit the document on Google Docs anymore!!!
    • GP will place a PDF and a Word version on Dropbox as soon as his transfer to LaTeX is ready. We can use the PDF to read/inspect, the Word version to edit with track changes and send our edits to GP.
  • We can start thinking about summarizing the report into scientific papers targeted at specific communities; first step is to identify suitable journals
    • biodiversity community: lead Edward and Nicolas
    • IT community: GP and Fabio

Next meeting

Thursday 12 June 2014, 10 am, changed to Friday 13 June 2014 due to Holiday in the Philippines on 12th.

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