GLOBAL BIODIVERSITY
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Global Biodiversity Information Facility
GLOBALBIODIVERSITY
INFORMATIONFACILITY
Hannu Saarenmaa
EC CHM & GBIF European Regional Nodes Meeting
Copenhagen, 2005-09-15/18
WWW.GBIF.ORG
The GBIF Data Repository Tool
(New updated version 3.0)
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Global Biodiversity Information Facility
OutlineOutline
1. Objectives and background
2. Design and installation
3. Use
4. Demonstration
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Global Biodiversity Information Facility
1. Objectives and background
1. Objectives and background
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Global Biodiversity Information Facility
Challenges in data sharingChallenges in data sharing
Eventually, all data sets become orphans: Archiving services are a necessity.
The concept ”share once, use many” requires available data repositories.
Data from archives must be available using standard mechanisms to portals such as GBIF.
IPR, confidentiality, and benefit sharing must be respected at all times.
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Global Biodiversity Information Facility
Goals of the GBIF Data Repository ToolGoals of the GBIF Data Repository Tool
Enable data custodians to manage their data and control its publishing.
Provide mechanism such that spreadsheets, etc., can directly be used for sharing data Hide the database complexities from users
Make available a simple data warehouse tool for those who want to host datasets for the community
I.e., lower the threshold of data sharing as low as possible.
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Global Biodiversity Information Facility
2. Design2. Design
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Global Biodiversity Information Facility
FunctionalitiesFunctionalities Data must be formatted according to the
Darwin Core standard and its extensions in flat spreadsheet format. In fact, any flat format will work (rows, columns)
The system will check and parse the data into embedded MySQL database that becomes available to the public as a DiGIR/TAPIR resource.
Owners can control the level of detail released: Fuzzying of geographic coordinates is available Collector names and time periods can be hidden Approval of terms and conditions for data use can be
required Owner can revoke release and update data. Metadata can be inherited to data to replace
missing values as defined. Includes an embedded image server
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Global Biodiversity Information Facility
Component architectureComponent architecture
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Global Biodiversity Information Facility
InstallationInstallation For Linux and Windows Based on Python, Zope 2.10 and
MySQL Supports the DiGIR and TAPIR
protocols of TDWG Turn-key installation Fits with directly into the EC CHM
software package
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Global Biodiversity Information Facility
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Global Biodiversity Information Facility
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Global Biodiversity Information Facility
3. Use3. Use
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Global Biodiversity Information Facility
Steps for data ownersSteps for data owners
1. Prepare the data files
2. Create a nested folder structure on the Repository for the collection
3. Enter default metadata scope (to cover missing values in data, etc.)
4. Decide on access policies
5. Upload the files
6. Publish the data files
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Global Biodiversity Information Facility
Create a collection and assign it to a data custodian...Create a collection and assign it to a data custodian...
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Global Biodiversity Information Facility
Enter metadata scope for the collection (inherited)Enter metadata scope for the collection (inherited)
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Global Biodiversity Information Facility
Create the resources (databases) of the collection and folders
Create the resources (databases) of the collection and folders
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Global Biodiversity Information Facility
Upload the files to folder, validate and release themUpload the files to folder, validate and release them
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Global Biodiversity Information Facility
Prepare the data file(s) in tab-separated formatPrepare the data file(s) in tab-separated format
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Global Biodiversity Information Facility
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Global Biodiversity Information Facility
Access policyoptions:•Fully open•Standard GBIF policy of acknow-ledgements•No direct download and fuzzying for web service access
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Global Biodiversity Information Facility
Data is now searchable locally and through the DiGIR/TAPIR protocols
Data is now searchable locally and through the DiGIR/TAPIR protocols
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Global Biodiversity Information Facility
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Global Biodiversity Information Facility
4. Demonstration
http://fmnh.eaudeweb.ro/
4. Demonstration
http://fmnh.eaudeweb.ro/