28. Diversity Workbench Workshop: How to organise and process biological data using GFBio services

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28. Diversity Workbench Workshop: How to organise and process biological data using GFBio services

The workshop is an official event of the 17th Annual Meeting of the Gesellschaft für Biologische Systematik. We address researchers who intend to organise, process and preserve their own biological raw data. They will come in contact with GFBio teams at three of the GFBio collection data centers, learn more about the Diversity Workbench (DWB), related services provided by the German Federation for Biological Data (GFBio) and how to import datasets in a relational database system appropriate to manage complex and heterogenous data. The number of participants is restricted to 15.

Organisation: Dr. D. Triebel, T. Weibulat (SNSB IT Center)

Location: Botanische Staatssammlung München with SNSB IT Center, Menzinger Str. 67, room no. 139, first floor

Date: 2016, February 24th

You do not need a laptop to participate in this workshop.

However, if you like to run the DWB training environment with model (example) datasets at home, please have your own laptop (MS Windows XP or later; .Net Framework 3.5 will be installed if necessary) with you. Mac users might consult the Recommendations for users with Non-Windows OS.

The DWB client software will be installed during the workshop. On request we will also install the DWB SQL databases for free. Model datasets for import will be available for download at this webpage.

First Topic: Collection and (Species) Occurrence Data (9:00-11:30 am)

Introduction and Demonstration: Dr. P. Grobe, B. Klasen (ZFMK), Dr. M. Weiss (SNSB)

  • Introduction GFBio/Data management
  • Data management in DiversityCollection
  • Use of templates for data
  • Ready to use import schemes (GitHubs SNSB, ZFMK)
  • DiversityCollection Import Wizard
  • Data publication (GBIF with DOI)

Model dataset for import:

Preview example datasheet

Download example datasheet: Example collection datasheet for GFBio

Download import scheme for DiversityCollection: Scheme for importing example collection datasheet for GFBio

Useful links:






Lunch Break: (11:30-12:30 pm), room no. 35, ground floor

Second Topic: Ecological Matrix Data (12:30-14:00 pm)

Introduction and Demonstration: Dr. D. Triebel, A. Link, V. Sanz, T. Weibulat (SNSB)

  • Introduction to data structures in DiversityDescriptions
  • Import of example data from SDD xml files
  • Import of CSV or Excel files with DiversityDescriptions Matrix Wizard
  • Import Wizard (e.g. for integration of additional data)
  • Data management in DiversityDescriptions
  • Data publication (in future via PANGAEA services with DOI or?)
  • Ready to use import schemes (GitHub SNSB)
Model dataset for import:

Download an example xml file with sample data (Morphological descriptions of some Ulmus species)

Download two example tables with ecological sample data (Biomass as description, Biomass as sample)

Useful links:



Coffee Break: (14:00-14:15 pm), room no. 35, ground floor

Third Topic: Checklists and Taxon Reference Lists (14:15-16:00 pm)

Introduction and Demonstration: Dr. J. Holstein, Dr. J. C. Monje (SMNS), Dr. M. Weiss (SNSB)

  • List import of text files
  • DiversityTaxonNames (=DTN) Import Wizard
  • Data management in DiversityTaxonNames
  • Use of taxon lists
  • Provision via DTN Rest Web Service
  • Provision via GFBio Terminology Server
  • Benefit of data publication with GBIF
Model dataset for import:

Download Albatrellaceae DTN taxon list (also provided with the client)

Useful links:



http://services.snsb.info/DTNtaxonlists/rest/v0.1/static/api-doc.html (up to now twenty two taxon lists with about 75.000 accepted "species" names)




http://www.gbif.org/publisher/0674aea0-a7e1-11d8-9534-b8a03c50a862 (up to now ten taxon lists)


Login details for the DWB Training Environment

  • IP-Address: training.diversityworkbench.de
  • Port: 5432
  • SQL-Server authentification
    • User: WORKSHOP
    • Password: available on request

Upcoming DWB Workshops

SNSB IT Center Upcoming Workshops