1. Flanders Marine Institute (VLIZ)
Kick Off meeting European Marine Observation and Data Network LOT NO: 5 – BIOLOGY WP6: Technical update EMODnet biological portal & link with other portals September 2013
Flanders Marine Institute (VLIZ)

2. WP 6: Technical update EMODnet biological portal & link with other portals
Objectives
1) to develop and maintain the EMODnet biological portal and portal services
2) to make the data, metadata and data products that are created and mobilized during the project available through the biological portal
Activities
1) Links and interoperability of the EMODnet Biology portal: The EMODnet biological portal will be able to provide links to metadata, data and data products for different systems by establishing direct machine-to-machine connections. The portal will be able to handle different data protocols for handling marine biological data by implementing different data standards.
2) Development of the portal: Portal components
Deliverables D6.1 Portal operational (Month 12) - D6.2: Portal fine-tuned for convergence with EMODnet central portal (M36) - D6.3: Maintenance of Portal (M12-M36)
EMODnet
June 26, 2018

3. Links and interoperability of the EMODnet Biology portal
Data Flow
IPT (DIGIR)
Custom services
OGC web services
File harvesting (CDI)
EMODnet
June 26, 2018

4. Links and interoperability of the EMODnet Biology portal
Integrated Publishing Toolkit - IPT (& DIGIR):
A freely available open source web application
Protocol based on Darwin Core standard
Managed by TDWG and used by Global Biodiversity Information Facility (GBIF) and the Ocean Biogeographic Information System (OBIS).
Manage and publish three types of data: taxon primary occurrence data, taxonomic checklists, resource metadata
Java-based web-application runs in standard web servers on Windows, Linux, Unix and Apple OS
Import from any common database, delimited text files (e.g. csv), or existing DarwinCore Archives
Distributed Generic Information Retrieval (DiGIR), an XML based web protocol used to support distributed data retrieval across remote biological collection databases and extensively used within the EurOBIS distributed database system.
EMODnet
June 26, 2018

5. Links and interoperability of the EMODnet Biology portal
A centralized EMODnet biology IPT will be set up
=> Partners can use it to publish their resources
Procedure
Step 1: Create your resource on the IPT
Step 2: Export your data
Step 3: Upload your data
Step 4: Map your data with Darwin Core
Step 5: Add metadata
Step 6: Publish your data
EMODnet
June 26, 2018

6. Links and interoperability of the EMODnet Biology portal
June 26, 2018

7. Links and interoperability of the EMODnet Biology portal
Custom services
Established data flow with data providers preparatory phase
SOAP/REST services
Example: ICES
EMODnet
June 26, 2018

8. Links and interoperability of the EMODnet Biology portal
File harvesting
Common Data Index (CDI)
Harvesting of data files described using Common Data Index in SeaDataNet infrastructure
CDI is the central discovery service in SeaDataNet, enabling users to have a detailed insight of the availability and geographical extent of marine data, archived at the connected data centres. It gives the description of individual data sets and measurements with key fields (what, where, when, how, who etc.).
Machine- to machine interface for automating selection of CDI and related data file requests
Biological Data Exchange Format
EMODnet
June 26, 2018

9. Links and interoperability of the EMODnet Biology portal
OGC Web Service
The geospatial data can be made accessible through the EMODnet biological portal through several OGC Web services.
Geospatial web services proposed by INSPIRE
Besides the Catalogue Service of the Web (CSW) which will enable access to metadata resources, three other OGC Web services will be implemented:
Web Feature Service (WFS). This service allows requests for geographic features across the Web. As such, the vector data on the portal can be transferred using this service.
Web Coverage Service (WCS). This service allows requests for gridded data across the web. As such, raster data of the portal can be transferred using this service.
Web Map Service (WMS). This service allows requests for maps across the web. As such, GIS maps of the portal can be transferred using this service.
A centralized EMODnet biology GeoServer for publishing geospatial data products
EMODnet
June 26, 2018

10. Development of the portal: Portal components
The biological data portal will build further on the biological data portal developed under the preparatory phase and available at This portal visualizes and makes data accessible through a unified search index. Data are available at three different levels of accessibility and precision
Metadata; Data ; Aggregated data
Increased Functionality for searching, viewing and extracting data
The spatial queries will be made possible by entering exact coordinates, by selecting a region on a geographic map or by selecting standardized sea areas; e.g. Exclusive Economic Zone’s (EEZs, IHO seas, marine regions defined by MSFD. The spatial query functionality will also allow users to search and select specific coastal information, based on the distance from the coastline
Search by biological and ecological attributes
Users will also be able to select metadata, data and data products from specific thematic and/or long-term monitoring datasets. The search interface will be developed to facilitate easy retrieval of these large thematic and monitoring data
User assistance and feedback, statistics and visibility
EMODnet
June 26, 2018

11. The portal functionalities
→ Data querying (taxa; parameters, datasets, layers)
Metadata
View List
Filter
Download
WoRMS
EMODnet
June 26, 2018

12. The portal functionalities
EMODnet
June 26, 2018

13. The portal functionalities
EMODnet
June 26, 2018

14. The portal functionalities
EMODnet
June 26, 2018

15. The portal functionalities
EMODnet
June 26, 2018

16. The portal functionalities
→ Data visualization
EMODnet
June 26, 2018

17. The portal functionalities
→ Data downloading
EMODnet
June 26, 2018

18. Thank you
EMODnet
June 26, 2018