01.08.2013 Biodiv

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Meeting Notes: call on Biodiv (Hangout)

Date: 01-Aug-2013


  1. Past week activity http://wiki.i-marine.eu/index.php/25.07.2013_Biodiv
  2. Name reconciliation progress
  3. Environmental enrichment requirements collection
  4. AOB


FAO: F.Fiorellato, A. Ellenbroek , CNR: P.Pagano, GP.Coro, IOC: W.Appeltans, Terradue: F.Brito, VUB: Edward Vanden Berghe, FIN: C.Aldemita


  1. Past week activity http://wiki.i-marine.eu/index.php/25.07.2013_Biodiv
    1. EvB: extra meeting http://wiki.i-marine.eu/index.php/26.07.2013_Biodiv; Nothing specific for today. Proposes to put calls on hold
    2. Nicolas / Casey will be travelling
    3. CNR will close for 3 weeks
    4. Next meeting: 29-Aug-12
  2. Name reconciliation progress
    1. NB Provided list of miss-spellings. Matched using speciMEn.jar, results from matching analyzed with R.
    2. EvB found some issues with way FB misspellings, and the source of the correctly spelled name are associated – they do not line up. Next week a meeting with EvB, FF and NB.
    3. GC: Can charts be explained?
    4. EvB: Action point 1. Explain graphs and charts in writing. Currently there is little effect of the choice of parser because the structure of the input was quite clear. The specific gain from Dima’s parser (‘GNI’) are hidden wrt the FAO parser (‘SIMPLE’). We need more test data, where the structure of the name is not as regular as in the present test sets. Parser should be able to pull out different parts of the complete name string (genus, epitheton, author, date…) and deal with these parts separately
    5. WA: Does the name matching include authority (author, year)?
    6. FF: not yet but on the to-do list
    7. CA/GC: CA’s matching tool (‘GSAy’) is ready, and is being tested in the infrastructure now
    8. EvB: GSAy will be tested and compared with output from Fabio’s SpeciMEn.jar using same R scripts as soon as appropriate
    9. Further work: create test datasets that would be more demanding of the parser; implement the parser as a separate ‘tool’ (or series of tools), a preprocessor that can be deployed independently of lexical matchers; create test data sets that would generate true negatives (now there are, in principle, only false negatives); automate report generation with Sweave;
  3. Environmental enrichment requirements collection
    1. EvB: Rost Parson of NODC sent an initial reply. Rost has mobilized staff and is actively seeking clarifications from iMarine. EvB suggests to suggest a conference call to understand how WOD data is transformed to atlas data. We need a clear and straightforward approach, and then decide who provides the interpolation tools.
    2. FB: Agrees to participate to such a call.
    3. Silent approval.
    4. AE mentions interest of group in FAO (not his own) in these activities; waiting for further details from them to see how we can help them.
    5. EvB: The conference call would be the best way to start, better than trying to assemble documentation through a long and tedious series of emails at this point.
    6. WA: Mentions the release of WOD with depth data in 2013
    7. FB: Has the BioOracle group been contacted?
    8. EvB: Their 2-dimensional approach is very good, but we need the 3d dimension, and over time. They use R extensively.
  4. AOB
    1. Discussion of possible involvement of CRIA in geographic data cleaning: deferred till Nicolas, who has been in touch with Vanderlei, can participate in conference call

Next call: 29-Aug-12 12.00 AM

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