1. Training course on biodiversity data publishing and fitness-for-use in the GBIF Network, 2011 edition
How Darwin Core Archives have changed the landscape of biodiversity data publishing
Presenter ( )
Role
Organization
Buenos Aires (Argentina)
28 September 2011

2. Background: Data Exchange
ABCD (TDWG Standard)
> 1200 concepts
XML
Shared via BioCase, Tapir
Darwin Core (pre-standard v. 1.2, 47 versions)
48 concepts, specimens
Shared via by DiGIR
Darwin Core (pre-standard v. 1.4)
46 concepts (plus extensions), specimens
Shared via Tapir
Darwin Core (TDWG Standard)
172 concepts (156 in Simple Darwin Core), biodiversity data
CSV, XML, RDF, JSON, …
Shared via Text files, Tapir, Darwin Core Archive…
- Reminder about the existing standards

3. Darwin Core Archive Primary Biodiversity Data Taxonomic Data Metadata

4. Darwin Core Archive Complete Package
Standard Darwin Core terms in a single, self-contained dataset
Taxon records or Occurrence Records
Data set metadata in EML
C'est le schméExplain the 3 components of an archive:
Core data file + optionnal extensions files
Metafile
Descriptor file

5. publishing data in the GBIF network
Darwin Core Archive:
Benefits
Simple format (text files)
Efficient harvesting (single file)
Efficient storage (compressed)
Easy access (no special software required)
Extensible (related files in one archive)
Simpler data transfer: 
what takes 500MB of data transfer in Tapir takes 3MB data transfer in DwC-A. 
Extensible format: more flexible way to map data
Preferred format for
publishing data in the GBIF network

6. Archives always have a metadata file as EML
Darwin Core Archive:
Anatomy
Archives always have a metadata file as EML
C'est le schméExplain the 3 components of an archive:
Core data file + optionnal extensions files
Metafile
Descriptor file

7. Ecological Metadata Language (EML)
For describing data sets – even unpublished ones
Title and Abstract
Citation and Attribution
Contact and Authors
Geographic Scope
Sampling Methods
Bibliography
and more…

8. Archives always have a core data file as text
Darwin Core Archive:
Anatomy
Archives always have a core data file as text
C'est le schméExplain the 3 components of an archive:
Core data file + optionnal extensions files
Metafile
Descriptor file

9. Records based on species occurrences – one per row
Core data file types
Records based on taxa – one species per row OR
Records based on species occurrences – one per row

10. Archives always have a core data file as text
Darwin Core Archive:
Anatomy
Archives always have a core data file as text
C'est le schméExplain the 3 components of an archive:
Core data file + optionnal extensions files
Metafile
Descriptor file

11. Core contains a “core ID” column, unique for every record in the file
Darwin Core Archive:
Anatomy
Core contains a “core ID” column, unique for every record in the file

12. Columns are matched to Darwin Core terms
Darwin Core Archive:
Anatomy
Columns are matched to Darwin Core terms

13. “Wingspan” is not a Darwin Core term
Darwin Core Archive:
Anatomy
Columns that do not match to a Darwin Core term may be included, but are ignored
“Wingspan” is not a Darwin Core term

14. 1) Rename columns in text file
Darwin Core Archive:
Anatomy
Two ways to match columns to Darwin Core terms
1) Rename columns in text file

15. 2) Match columns to terms in a separate meta.xml file
Darwin Core Archive:
Anatomy
Two ways to match columns to Darwin Core terms
2) Match columns to terms in a separate meta.xml file

16. Darwin Core Archive: Anatomy meta.xml matches the columns
in the core data file (species.txt)
More on how to make the meta.xml file later…

17. Archives can include extension files
Darwin Core Archive:
Anatomy
Archives can include extension files
Species.txt
Extensions link to the core through the core ID
Common_names.txt
Extensions allow multiple records to be linked to a core record.

18. GBIF hosts extension definitions

19. Multiple extensions files can be linked to the core
Darwin Core Archive:
Anatomy
Multiple extensions files can be linked to the core

20. Darwin Core Archive:
Anatomy
All files are stored in a single folder

21. Darwin Core Archive: Anatomy The folder is zipped. Data files
Column matching file
Data set documentation
This is a Darwin Core Archive

22. Darwin Core Archive: Publishing
/my_data.zip
Archives on a web server can be accessed by a URL.
Share this URL to “publish” your data!

23. Darwin Core Archive:
Publishing Options

24. GBIF Spreadsheet Templates

25. Integrated Publishing Toolkit

26. Data Hosting Centers

27. Darwin Core Mapping Assistant
Metafile

28. Darwin Core Mapping Assistant

29. Darwin Core Archive: Publishing Options
GBIF Darwin Core Archive Spreadsheet Templates:
data in a spreadsheet already
simple archive authoring
IPT:
creating/managing archives for multiple data sets
managing archives for multiple organisations
metadata as GBIF Metadata Profile of EML
Make Your Own:
automating archive generation
customisation
Hosting center:
economy of scale
Infrastructure and support
Combinations…
Explain the 3 components of an archive:
Core data file + optionnal extensions files
Metafile
Descriptor file

30. Training course on biodiversity data publishing and fitness-for-use in the GBIF Network, 2011 edition
How Darwin Core Archives have changed the landscape of biodiversity data publishing
Presenter ( )
Role
Organization
Buenos Aires (Argentina)
28 September 2011