05.04.2012 Biodiversity Cluster Conference Call

From IMarine Wiki

Jump to: navigation, search



Time: Thursday April 05, 2012, 16:00 - 17:30 Europe/Rome


CNR: L. Candela, D. Castelli, G. Coro, P. Pagano

FAO: A. Ellenbroek

FORTH: Y. Marketatis

FIN: N. Bailly

UNESCO: E. Vanden Berghe

CRIA: V. Canhos


OBIS Database migration

The OBIS Steering Group has to decide on this discussion item.

Taxon Service

The scope of this service seems to be quite quite large (actually this is Species Service in Lino's email). It contains at least 4 components.

  • apart from the name of the service, CNR clarified that he plans to develop four services on biodiversity data access:
    • ...

We should start involving in the discussions ITIS, NCBI and IRMNG.

One of the expected services is the Taxon Names Access.

One of the expected services is Taxon Name Reconciliation.

  • Edward is using a set of SQL statements to merge two taxonomic lists. This is a sort of encoding of a number of rules driving lists merging.
  • the proposed service produces a list of pairs of Taxa each with a probability of similarity among the two Taxa;
    • CNR is looking at the Taxamatch service (this is a source of rules);
    • FIN: Taxamatch is implemented in other languages by others, Heimo Rainer, Mike Giddens, ...;
    • Carla Ortiz (FIN) has worked on the algorithm of Taxamatch, she can be integrated in the loop;
    • FIN will take the leadership of specifying services for Taxon Data;
  • Re data availability:
    • this depends on the number of plugins the infrastructure is equipped with, one plugin for each data source / provider;

CNR current schedule is the following:

  • first work on occurrence points, i.e. work on services giving access to occurrence points from a number of data providers;
  • in a second phase work on taxonomic data;

On the Occurrence Data Reconciliation:

  • we have access to OBIS e GBIF through the 'occurrence service';
  • we have to consider how to re-use the 'occurrence service' for 'singleton'/'duplicate' identification;
  • further thinking is needed by Edvard;
  • CNR plans to work on it from May 1st on; By end of April CNR will complete the activity on 'occurrence point access';
    • the enrichment will come in a successive phase, since this depends on results of other clusters (namely the Geo-spatial one);
  • Vanderlei: for outliers flagging you need gazetteers
    • CNR relies on some gazetteers for flagging occurrence points. BTW, this might be another service to use;
    • Edward: VLIZ has a gazetteer;
    • Edward: btw, this is related to data enrichment, we might postpone the discussion;
  • CNR would like to have guidance/help on how to classify Occurrence Points, e.g. survey rather than specimen; This classification is fundamental for their exploitation;
    • Edward will describe the types of occurrence points;

ACTION: A wiki page for each of the 5 identified services (occurrence data access, occurrence data reconciliation, occurrence data enrichment, taxon name discovery, taxon name reconciliation) might be created. This should contain requirements and information.

  • Re occurrence points we have identified tasks for CNR and Terradue (Geospatial);
  • The FAO team should contribute, namely on the part of reconciliation;
  • a clear development plan should be defined including responsibilities;

GP Discussion pages

This is the page created by Gianpaolo http://wiki.i-marine.eu/index.php/Taxa_Merging_Discussion

The first version has been produced by Edward. Nicolas should contribute to this.

A separate page should be created for documenting the rules.



Agreed actions

  • five services have been identified; A wiki page aiming at specifying each of them should be created;
  • FIN team will take the leadership of specifying the two services related to Taxa Names;
Personal tools