24.04.2014 BiolDiv

Meeting 24 April 2014, 10:00 am

Google Hangout

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

Notes

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

Friday 02 May 2014, 10:00 am European time.