GLOBAL BIODIVERSITY

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)


OutlineOutline

1. Objectives and background

2. Design and installation

3. Use

4. Demonstration





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.


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.


2. Design2. Design


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


Component architectureComponent architecture


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




3. Use3. Use


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


Create a collection and assign it to a data custodian...Create a collection and assign it to a data custodian...


Enter metadata scope for the collection (inherited)Enter metadata scope for the collection (inherited)


Create the resources (databases) of the collection and folders

Create the resources (databases) of the collection and folders


Upload the files to folder, validate and release themUpload the files to folder, validate and release them


Prepare the data file(s) in tab-separated formatPrepare the data file(s) in tab-separated format



Access policyoptions:•Fully open•Standard GBIF policy of acknow-ledgements•No direct download and fuzzying for web service access


Data is now searchable locally and through the DiGIR/TAPIR protocols

Data is now searchable locally and through the DiGIR/TAPIR protocols



4. Demonstration

http://fmnh.eaudeweb.ro/

4. Demonstration

http://fmnh.eaudeweb.ro/

Documents

GLOBAL BIODIVERSITY