Contributing data - the data submission process

To contribute data to EMODnet Seabed Habitats, the data must be in a standardised ingestible format to allow it to be combined with datasets from other organisations.

Please note: ALL GIS data must be supplied in shapefile (.shp) format.

The following steps should be undertaken when submitting habitat maps to EMODnet Seabed Habitats. The required files and an explanation of the steps for offline viewing are available in the downloadable data provider package available at the bottom of this page.

To view/hide the guidance for undertaking a step, please click on the relevant heading.

If you have any concerns or questions, please .

An important field in the habitat map attribute table is the globally unique identifier (GUI), which is a unique code identifying a dataset (e.g. a single habitat map).

The GUI consists of a 2-letter county code (which corresponds to ISO3166-1) followed by 6 digits. For example, a dataset from Italy would be written IT000005. The final 6 characters can be used freely although we suggest sequential numbering of datasets to help prevent duplication.

To ensure each GUI is unique, here are some suggested GUI ranges for organisations that have previously submitted data:

Table1: Suggested GUI ranges for existing organisations
Partner GUI
Ifremer (France) FR000001 to FR001999
IMA (France) FR002000 to FR002999
DREAL (France) FR003000 onwards
Universidade do Algarve (Portugal) PT000001 to PT000999
Universidade de Aveiro (Portugal) PT001000 to PT009999
IPIMAR (Portugal) PT010000 to PT099999
Universidade dos Açores (Portugal) PT100000 onwards
AZTI (Spain) ES000001 to ES000999
IEO (Spain) ES001000 onwards
Marine Institute (Republic of Ireland) IE001000 onwards

 

Warning: Each GUI must be unique to an individual survey or habitat map and must not be re-used.

If your organisation is not in the list above, then please , and we will direct you to your country's project partner who will supply you with GUI codes. The GUI will be used in the shapefile's attribute table and as the 'Alternate Title' field in the metadata record created in Step 3.

All shapefiles provided to EMODnet Seabed Habitats must be supplied in the WGS84 unprojected coordinate system (EPSG:4326).

If your habitat map is not in this coordinate system, then it must be reprojected before continuing with the data submission. Within ArcGIS, for example, this can be performed using the "Project" tool.

To ensure that your map data can be properly integrated in composite datasets, and to allow the data to display properly, the shapefile should be cleaned to remove any geometry or topology errors. For more information on how to clean the shapefile, please read "EMODnetSBH Supplying data - GIS tips" (PDF, 283KB) from the data provider package.

Finally, the supplied habitat shapefile should be named as its GUI. For example, a habitat map with GUI "IT000005" should be named as "IT000005.shp".

To enable habitat maps from different sources to be compared and combined into the large datasets used in EMODnet Seabed Habitats and displayed on the interactive map, the map’s attribute table must be converted into a standardised format. We call this a Data Exchange Format (DEF).

For the purposes of EMODnet Seabed Habitats, data are required to be submitted in an updated version of the MESH DEFs as they provide a tried and tested method of standardising maps for collation and conflation.

There are two possible habitat data exchange formats, dependant on the habitat map itself, described on the Data Exchange Formats page and downloadable (PDF, 268KB) within the data provider package.

The map should first be converted into the Original Habitat DEF. If the map is detailed enough to be translated into the EUNIS classification system, or is already in EUNIS classification, the attribute table should be extended into the Translated Habitat DEF and the habitats translated. If the map represents habitats from Annex I of the EU's Habitats Directive (for Natura2000 sites), the attribute table should be extended into the Habitats Directive DEF.

The values for the fields in the DEF should be entered as per the Data Exchange Format guidance. Mandatory fields must contain a valid value for each feature/polygon, non-mandatory fields need not contain values but the field itself must still exist in the final submission for the data to be valid.

If the original habitat map does not contain many polygons, it should be viable to enter the DEF field values manually. If the habitat map contains a number of habitats repeated within a large number of polygons, an attribute join can be used to fill the HAB_TYPE and T_RELATE fields with less effort. A possible method of doing this is outlined in "EMODnetSBH Supplying data - GIS tips" (PDF, 283KB) from the data provider package.

Once converted into the required DEF, the final attribute table should contain all of the DEF’s fields, and all extraneous fields should be removed.

Python scripting

If you have ArcMap and are comfortable with python, the change to the DEF schema can be automated by using either of two python scripts available in our GitHub repository. The script to use depends on your habitat map:
"add_MESH_ORIG.py" adds all fields required by the Original Habitat DEF.
"add_MESH_TRANS.py" adds all fields required by the Translated Habitat DEF.

After translation, extraneous fields may either be deleted manually, or by using either of two python scripts supplied in the data provider package. Again, the script to use depends on your habitat map:
 "trim_MESH_ORIG.py" removes all fields not required by the Original Habitat DEF.
 "trim_MESH_TRANS.py" removes all fields not required by the Translated Habitat DEF.

The scripts provided will act on all shapefiles within a folder or location provided by the user, and so can be used to batch-process addition and removal of fields with multiple maps.

Warning: It should be noted that due to the behaviour described above, maps to be translated must moved into their own folder before running the scripts to avoid affecting any other shapefiles.

Note: This step does not need to be completed if submitting a habitat map in the Habitats Directive DEF.

EMODnet Seabed Habitats uses the "MESH confidence assessment" method for determining a dataset-level confidence value determined by the processes and data that were used to create the habitat map. This was developed during the Mapping European Seabed Habitats project which ran from 2004 to 2008.
See the MESH Confidence Assessment Scheme section of the archived MESH Mapping Guide for further guidance about how to conduct a confidence assessment.

A confidence assessment should be carried out for each habitat map, EMODnet Seabed Habitats uses the MESH confidence scoring technique. The spreadsheet "EMODnetSBH Confidence assessment scoresheet" (XLS, 133KB) in the data provider package contains a template for this.

The first sheet ("Score sheet") is the only sheet requiring input, and the scores for the categories should be entered in columns B to P, with the corresponding map’s GUI in column A.

The second sheet ("Weightings") contains values used in the calculation of the final score and can be left untouched.

Sheets three to five ("Remote Sensing", "Ground truthing", Interpretation") explain the scoring for each categories on sheet one and should be read before undertaking the scoring process. The same information can be found within the accompanying document "EMODnetSBH Confidence assessment guidelines" (PDF, 151KB).

Scores for multiple habitat maps can be entered on a single spreadsheet, and it is advised that this is done when it is expected that a package of multiple maps will be delivered. The scoring for each subsequent map should be entered on a new row, with its GUI entered into column A.

You can also use the online MESH confidence Tool to generate scores and export a CSV text file that can be imported into the confidence spreadsheet.

For each habitat map (GUI), a rectangular "Study Area" geographic bounding box should be created, encompassing the surveyed areas. The sides of the bounding box should be precisely horizontal and vertical when viewed unprojected in WGS84. In ArcGIS, this can be performed using the "Minimum bounding geometry" tool selecting "ENVELOPE" as the "Geometry Type", and grouping by the "GUI" field.

The resulting rectangular feature should look similar to Figure 1 (below).

Example of a geographic bounding box

Figure 1: An example habitat map (solid colours representing habitat types) and its respective Study Area polygon (red outline) viewed in unprojected WGS84.

 

The study area feature class should contain only one feature and must be supplied in the Study Area DEF described on the Data Exchange Formats page and downloadable (PDF, 92KB) within the data provider package.

The feature should be saved as a shapefile with the naming format of "[GUI]_StudyArea.shp". For example, the Study Area for habitat map GB012345 should be saved as "GB012345_StudyArea.shp"

When these outlines are combined by EMODnet Seabed Habitats, the layer can be used to display map extents and confidence scores.

Python scripting

If you have ArcMap and are comfortable with python, the creation of habitat map study areas can be automated by using the python script "studyarea_creator.py" available in our GitHub repository.

The script should be run on a folder containing only habitat maps that are formatted and named in accordance to steps 2 and 3.

The script will produce a correctly named shapefile in the Study Area DEF. The GUI value will be filled in automatically, but the confidence score for the map must be entered into the SUM_CONF field manually.

For EMODnet Seabed Habitats,  metadata will be entered into the online habitat mapping metadata catalogue maintained by the International Council for the Exploration of the Seas (ICES) on behalf of its Working Group on Marine Habitat Mapping (WGMHM). The main purpose of this site is for working group members to upload metadata about all habitat mapping activity that had occurred in the previous year.

You should supply your habitat map’s metadata to your country’s partner in .xml format. The metadata that you create should conform to the EU’s INSPIRE metadata standard.

When creating your metadata, it is critical that the "Alternate title" is equal to the map’s 8 digit GUI reference code. This is so that the interactive map can communicate with the metadata catalogue.

There are many tools available to help you write metadata.

Within ArcCatalog:

  • Open ArcCatalog and navigate to shapefile requiring metadata
  • Open ArcCatalog options, and ensure that "INSPIRE Metadata Directive" is selected as the Metadata Style inside of the Metadata tab
  • Click on the Metadata or Description tab
  • Click Edit and fill in metadata
  • Save the metadata

Other local or online metadata editor tools:

You may be familiar with another tool for filling in metadata and exporting an XML file; if so you may use this. Ideally, it should produce INSPIRE-compliant metadata.

The Data Provider Agreement template (DOC, 158KB) contained within the data provider package should be completed for each habitat map to be supplied to EMODnet Seabed Habitats. Multiple habitat maps may be entered on one form, with each habitat map as a "Dataset" named by its GUI code.

If the dataset does not originate from your organisation, please enter the name of the owner in the relevant column so that they may be attributed properly.

Any usage limitations should be described in sections 2.3, and section 3 should be filled in if necessary.

Once completed, sign the form and include it within the data package to be sent to your country's EMODnet Seabed Habitats project partner.

The GIS data (in ESRI shapefile format), confidence assessment spreadsheet, metadata (in .xml format) and signed data provider agreement should then be sent to your country’s project partner. Please and we will direct you to your country's partner who will handle your data submission.

The partner will then periodically consolidate data packages and:

  1. Enter metadata for each habitat mapping dataset into the ICES metadata catalogue
  2. Send shapefile datasets corresponding to the metadata to JNCC for addition to the webGIS – habitat map layer and study area layer.
  3. Send a single confidence assessment spreadsheet to JNCC for addition to the webGIS containing information for all maps in the package.
  4. Send data provider agreement to JNCC for archiving.

JNCC will then upload the GIS and confidence data to the EMODnet Seabed Habitats webGIS.

The procedure is summarised in Figure 2 below.

Flow diagram describing data contribution to EMODnet Seabed Habitats

Figure 2: EMODnet Seabed Habitats webGIS data flow.

File Size (kb) Type
EMODnetSBH Complete data provider package (contains all files below) 1652 .zip
      EMODnetSBH Preparing habitat data for submission 445 .pdf
      EMODnetSBH Data Exchange Formats 268 .pdf
            EMODnetSBH Original Habitat DEF 74 .pdf
            EMODnetSBH Translated Habitat DEF 150 .pdf
            EMODnetSBH Habitats Directive DEF 32 .pdf
            EMODnetSBH Study Area DEF 136 .pdf
      EMODnetSBH Confidence assessment scoresheet         133 .xls
      EMODnetSBH Confidence assessment guidelines 151 .pdf
      EMODnetSBH Data Provider Agreement    158 .doc
      EMODnetSBH Supplying data - GIS tips 283 .pdf
EMODnetSBH Python scripts at the EMODnet seabed habitats GitHub repository    
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