EDIT WP5 Platform for Cybertaxonomy

The prototype service to generate printed publications from the CDM (Printservice) consists of an interface that lets a user select a classification or specific parts of a classification, a system to harvest the required data from the CDM REST Services (Webservice) and XSL stylesheets to process the acquired data into the Open Document Format (ODF). Being a prototype, the system does not claim to be complete, correct or useful in production use.

The Pan European Species directories Infrastructure (PESI, www.eu-nomen.eu/pesi/) develops and integrated access system to the three major European taxonomic checklists Euro+Med PlantBase (ww2.bgbm.org/EuroPlusMed/), Fauna Europaea (www.faunaeur.org/), and the European Register of Marine Species (ERMS, www.marbef.org/data/erms.php). Additional European checklists will follow as soon as the basic infrastructure has been established.

This report is based on Skype and Chatzy talks that took place on the 26^th of March 2010 as well as e-mail correspondence on the EDIT Geo developers mailing list. It was compiled by Marcin Gąsior (MIZPAN) with a generous input from Patricia Mergen (RMCA) , James Davy (RMCA), Franck Theeten (RMCA), Alexander Kroupa (MFN) and the colleagues from the EDIT developer mailing list.

This report describes the methods of inventory completeness assessment developed in the EDIT geoplatform tools and presents a spatial analysis based on ATBI data. It has been compiled by Marcin Gąsior (MIIZPAN) with a generous input from Pere Roca Ristol (CSIC), Alexander Kroupa (MFN), Patricia Mergen (RMCA) and the colleagues from the EDIT developer mailing list. The incompleteness of species inventories due to limited field sampling is considered as an important issue in many biodiversity studies.

The present component details the collaboration between the activity 5.6 (description and keys) and an EDIT exemplar group (the Cichorieae exemplar group). For activity 5.6, the aim of this collaboration is the visibility of the integration of descriptive data into the EDIT Common Data Model (CDM). For the Cichorieae exemplar group of the WP6, this collaboration could help to get the best of their descriptive data and better fit the needs of the Cichorieae Dataportal website users.

The prototype of the references index (GBV demonstrator for the EDIT/BHL-Europe GRIB) was built by the German common library network GBV (Gemeinsamer Bibliotheksverbund, Göttingen). It allows users to browse and search titles held by libraries of EDIT member institutions and will include library catalogue data from BHL-Europe/BHL institutions in the future.Test sets from FUB-BGBM, MFN, NNM Naturalis and NHML have been imported into and are in the process of being deduplicated within the GBV demonstrator.

Descriptive data are one of the most important categories of information produced by taxonomists when describing new species or performing taxonomic revisions. This is why the EDIT Common Data Model (CDM) is designed to include and store descriptive data. SDD is the current TDWG (Biodiversity Information Standards) standard for descriptive data. Most of the existing software managing descriptive data (e.g. Lucid, Xper², DiversityDescription) already support it, allowing their users to import or export descriptive datasets.

Due to the lack of quality and incompleteness of significant part of biological information research on biodiversity can be biased. Additional surveys directed to fill in all gaps in knowledge and recover a reliable picture of the distribution for highly diverse taxa are impossible to conduct because of limited time and resources. That is why alternatives to assess the reliability and/or enhance the information currently stored in biodiversity databases are preferred

The EDIT contract and consortium agreement specify that software produced in the project will be put under a public license and be distributed as open source. Sustaining the EDIT Platform thus means supporting the open source environment that allows maintenance and further development of the Platform. All partners involved in Platform software development are committed to attracting further project funding to improve the Platform, and some such projects are already in place (PESI, SYNTH¬ESYS II, BHL-Europe) and an increasing number of applications are being submitted.

This report describes application to map inventory completeness. The main conclusions raised by report C5.35 & C5.38 are that:
1. current species distribution information is biased and insufficient for most taxonomic groups
2. modelling methods can not provide reliable and useful distribution predictions if they are based in these biased of data.”
For that reason key tools to implement were identified which allow to:
1. examine the degree of completeness of distributional information,