24.04.2014 BiolDiv

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Meeting 24 April 2014, 10:00 am

Google Hangout

Present: Fabio, Nicolas, Casey, Edward, Anton, Gianpaolo



BiOnym paper

  • Review of various papers collected by Edward and Anton.

In particular Boyle et al. 2013 in BMC Bioinformatics about a taxon nema matching they developed for plants.

Apparently a mix between the GNI parser, and the Tony's Taxamatch. To explore if there are improvements over Taxamatch or if it is only an effect of linking GNI parser + Taxamatch.

  • Finish section 2 and 5 for the next week call (Edward, Nicolas, Fabio).
  • Comparison with same systems in other domain, e.g., vessel names.
  • GP to modify section 3 and 4.
  • Intro of section 3.5: It is the restricted matching running process workflow, not the overall BiOnym conceptual workflow, so can be kept here.
  • Complete the point 5.6 in the discussion about how we evaluated the performance (Edward). But still to evaluate if not better in 4.4.
  • Discussion on details of reporting (to complete if necessary).
  • Section 4: 3 paragraphs as section 3.4 (GP or Edward).
  • Should we move the paragraph on parser comparison to discussion? To be evaluated (Fabio).

User Interface

  • Machine set up in CNR but there is an issue about MySQL 5.6 comparatively to 5.5. Should be running on Friday 25.
  • Is it Apache or TomCat? Casey has to explore what is the best. CNR install Apache, and explore if TomCat can be also.

Next meetings

Thursday 1 May 2014, 11:00 am European time.

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