2nd EU BON training on data
sharing tools
Demonstration of GBIF/EU BON IPT for
monitoring networks
Larissa Smirnova
Royal Museum for Central Africa
2nd EU BON training, Joensuu 19 March 2015
The EU BON Integrated Publishing Toolkit
Presentation structure:
 What is IPT and why IPT?
 Why sample-based data?
 Example of data from CS portal
 How to publish data with EU BON IPT
 IPT metadata editor
 DwC mapping
 Publication of resource
 Useful links
 Acknowledgments
2nd EU BON training, Joensuu 19 March 2015
GBIF Integrated Publishing Toolkit (IPT)
 Developed to facilitate the integration of
biodiversity data from
heterogeneous sources using common standards and protocols.
 Differs from previous systems (TAPIR, DiGIR, BioCase) by new
functionalities:
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Ability to transfer big amounts of records
High speed of indexing process
Additional benefits and services for the data (i.e. public web interface to
browse/expose (meta)data or mapping services)
Ability to publish certain types of biodiversity data, such as names
checklists and dataset metadata.
Data quality assessment tools
Increased data exchange using globally accepted formats (i.e. OGC web
services)
Easy ways to monitor data access and use for the different resources
connected to the GBIF Network….
Since February 2015 (yet for testing only):
• Possibility to assign DOIs to resources
• Auto-generation of a citation for a resource including the version number
and DOI
• Machine readable license
2nd EU BON training, Joensuu 19 March 2015
Key functionality of v2.0:
‣User management
(administrator, manager, general user)
‣Extension management
(data extensions, vocabularies)
‣Institution management
(select institutions hosting IPT or sharing
datasets)
‣Configuring datasets
‣Managing dataset state
(private, public or registered)
‣Interfaces (DwC-A, EML)
2nd EU BON training, Joensuu 19 March 2015
Museum
What can you publish with IPT?
Biological station
Monitoring
Collection
Researcher
 Primary biodiversity data
 Species name information
Scientific
database
 Dataset description (metadata)
 Sample-based data
2nd EU BON training, Joensuu 19 March 2015
Online
database
Why sample-based data?
Museum data
Collection data
Research data
Biological stations
Monitoring programs
Citizens with apps
Monitoring data
Occurrences, checklists
Occurrences
Checklists
Taxon core
Occurrence core
Event core
Taxon core
Occurrence core
2nd EU BON training, Joensuu 19 March 2015
EU BON IPT: http://eubon-ipt.gbif.org/
+ Sample core and extensions
In future: data paper publishing possibility
2nd EU BON training, Joensuu 19 March 2015
Example of sightings from Waarnemingen.be
2nd EU BON training, Joensuu 19 March 2015
Example of sighting and
csv table of dataset from
Waarnemingen.be
2nd EU BON training, Joensuu 19 March 2015
7-step guide to data publication by Canadensys
1. Create your resource on the IPT
2. Export
3. Upload
4. Darwin Core mapping
5. Add metadata
6. Publish
7. Register with GBIF
2nd EU BON training, Joensuu 19 March 2015
IPT installed?
No
Installation guide
Installation video
IPT workbook and
sample datasets
Yes
Do you have a user account?
No
Ask administrator of
the IPT to create a
new account for you
([email protected]
for EU BON IPT)
Yes
Log in to start
If you have trouble installing the tool, check the IPT project site (code.google.com/p/gbifprovidertoolkit/) or join the IPT mailing list (lists.gbif.org/mailman/listinfo/ipt) and interest group
(community.gbif.org/pg/groups/3529/) or contact the GBIF Secretariat via [email protected].
2nd EU BON training, Joensuu 19 March 2015
login -> create new ressource -> choose type
Optinal « choose file » is
used for exchange of data
between two IPTs. If you
have DwC-A file you can
browse it here.
2nd EU BON training, Joensuu 19 March 2015
IPT metadata editor
2nd EU BON training, Joensuu 19 March 2015
2nd EU BON training, Joensuu 19 March 2015
Geographic Coverage
2nd EU BON training, Joensuu 19 March 2015
Taxonomic Coverage
2nd EU BON training, Joensuu 19 March 2015
Temporal Coverage
2nd EU BON training, Joensuu 19 March 2015
Keywords
http://rs.gbif.org/vocabulary/
2nd EU BON training, Joensuu 19 March 2015
GBIF vocabulary: http://rs.gbif.org/vocabulary/
2nd EU BON training, Joensuu 19 March 2015
Add a source data file
2nd EU BON training, Joensuu 19 March 2015
Start mapping source data
2nd EU BON training, Joensuu 19 March 2015
Data Mapping
DwC terms
Data source field select box
Constant value text box
2nd EU BON training, Joensuu 19 March 2015
Mapping
preview
2nd EU BON training, Joensuu 19 March 2015
Mapping preview
2nd EU BON training, Joensuu 19 March 2015
Three traps:
Example of sample-based data
UV tube 2 x 80 W 1500 mm
funnel trap
Soil-type light trap with
250W Hg clearlamp upward
Jalas-model light trap with 125W Hg clear lamp
2nd EU BON training, Joensuu 19 March 2015
Data collected from three light traps for moths
Access database:
observationSiteEvents, with the traps (siteID) and the time
periods they operated (observation ID) -> event core
observationCatches, which is the occurrences
(occurenceID)at each trap and period -> occurrence extension
2nd EU BON training, Joensuu 19 March 2015
Query -> Tab delimited text file
2nd EU BON training, Joensuu 19 March 2015
2nd EU BON training, Joensuu 19 March 2015
Ptoblem with decimalLattidude is coma
Change it to dot
2nd EU BON training, Joensuu 19 March 2015
DwC mapping
2nd EU BON training, Joensuu 19 March 2015
DwC mapping
2nd EU BON training, Joensuu 19 March 2015
DwC-A assistant
http://tools.gbif.org/dwca-assistant/
2nd EU BON training, Joensuu 19 March 2015
Value translation
2nd EU BON training, Joensuu 19 March 2015
Publishing of resource
Publish -> EML, RTF, DwC-A
“Publish” button will be activated if:
• the required metadata for the
resource are complete,
• the user has the role "Manager
with/without registration rights“
• publishing organisation is
registered in the GBIF registry
(password must be known)
2nd EU BON training, Joensuu 19 March 2015
Resource is published but not yet registered!
2nd EU BON training, Joensuu 19 March 2015
Publishing of resource
By default, resource is visible only
to the user who created it and
Admin.
Change it to open (public), or
discoverable through the GBIF
Registry (registered). The last one
is not possible on test IPT.
2nd EU BON training, Joensuu 19 March 2015
Resource Registration Options
• Darwin Core Archives in IPT
GBIF
• Others
• Darwin Core Archives not in IPT
• DiGIR. Tapir, BioCASE
http://tools.gbif.org/dwca-register/
2nd EU BON training, Joensuu 19 March 2015
IPT
GBIF resources:
Installation guide:
https://code.google.com/p/gbif-providertoolkit/wiki/IPT2ManualNotes
Installation video:
https://vimeo.com/116142276
IPT workbook and sample datasets:
http://www.gbif.org/resource/81211
IPT v2 User Manual:
http://code.google.com/p/gbif-providertoolkit/wiki/IPT2ManualNotes
Occurrence Data Publishing Tutorial :
http://code.google.com/p/gbif-providertoolkit/wiki/TutorialOccurrenceResource
PUBLISHING-DWCA-IPT-kyle.pdf
DwC-A assistant:
http://tools.gbif.org/dwca-assistant/
Terms Used in Bionomenclature. The naming of organisms (and plant communities):
http://www.gbif.org/resources?search_api_views_fulltext=bionomenclature&sort_by=gr_date_of_publication&sort_order=DE
SC&items_per_page=20
How to register datasets with GBIF: http://www.gbif.org/resource/81802
2nd EU BON training, Joensuu 19 March 2015
Thanks to:
Éamonn Ó Tuama: Metadata publishing with the IPT, 2011
Tim Robertson: The Pathway to the Integrated Publishing Toolkit version 2, 2011
Kyle Brake presentation on publishing with IPT:
http://biodiversity-informatics-training.org/wp-content/uploads/2013/09/PUBLISHING-DWCAIPT-kyle.pdf
Canadensys guide to data publication: http://www.gbif.org/resource/81189
John Wieczorek presentation “How to register data sets with GBIF”:
http://www.gbif.org/resource/81802
2nd EU BON training, Joensuu 19 March 2015