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
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
Step 1: Assign a
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
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
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
||FR000001 to FR001999
||FR002000 to FR002999
|Universidade do Algarve (Portugal)
||PT000001 to PT000999
|Universidade de Aveiro (Portugal)
||PT001000 to PT009999
||PT010000 to PT099999
|Universidade dos Açores (Portugal)
||ES000001 to ES000999
|Marine Institute (Republic of Ireland)
Warning: Each GUI must be
unique to an individual survey or habitat map and must not be
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
Step 2: Prepare the
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
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
Supplying data - GIS tips" (PDF, 283KB) from the data
Finally, the supplied habitat shapefile should be named as its
GUI. For example, a habitat map with GUI "IT000005" should be named
Step 3: Standardise the
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
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
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.
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
"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
"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
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.
Step 4: Confidence
Note: This step does not need to be completed if
submitting a habitat map in the Habitats Directive
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
Habitats project which ran from 2004 to
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
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
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
Step 5: Create a Study
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
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).
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
When these outlines are combined by EMODnet Seabed Habitats, the
layer can be used to display map extents and confidence scores.
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
The script should be run on a folder containing only habitat
maps that are formatted and named in accordance to steps 2 and
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.
Step 6: Create the
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
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.
- Open ArcCatalog and navigate to shapefile requiring
- Open ArcCatalog options, and ensure that "INSPIRE Metadata
Directive" is selected as the Metadata Style inside of the Metadata
- Click on the Metadata or Description tab
- Click Edit and fill in metadata
- Save the metadata
Other local or online metadata editor
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.
Step 7: Complete the
data provider agreement
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
Step 8: Submit the data
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
The partner will then periodically consolidate
data packages and:
- Enter metadata for each habitat mapping dataset into the ICES
- Send shapefile datasets corresponding to the metadata to JNCC
for addition to the webGIS – habitat map layer and study area
- Send a single confidence assessment spreadsheet to JNCC for
addition to the webGIS containing information for all maps in the
- 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.
Figure 2: EMODnet Seabed Habitats
webGIS data flow.
EMODnet Seabed Habitats
data provider package