Submission process for contributing habitat maps

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 contact us

  • Step 1: Assign a GUI

    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.

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

    If you are unsure about which GUIs are available then please contact us and we will direct you to your country's project partner who will supply you with some 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.

  • Step 2: Prepare the shapefile
    File Type Last Modified
    Guidance: Supplying data - GIS tips .pdf 28/11/2019
    Guidance: Areas with more than one habitat type .pdf 14/12/2017

    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 'Guidance: Supplying data - GIS tips' (see above).

    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".

    In some cases, you may have more than one habitat assigned for a single area, for example where more than one habitat is known to exist in a heterogeneous area, but cannot be delineated, or where two habitats may exist as a result of vertical stratification. This should be represented in a specific way in order to comply with the INSPIRE Directive - see 'Guidance: Areas with more than one habitat type' (above).

  • Step 3: Standardise the attribute table
    File Type Last Modified
    Guidance: Data Exchange Formats .pdf 20/01/2020
    Template: Data Exchange Formats .shp 27/02/2020
    Tool: Python scripts for formatting to the Data Exchange Format [link to Github] 23/03/2020

    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 the downloadable PDF (see above).

    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 Natura 2000 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 the supplying data guidance document (see step 2).

    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.

    Automating using Python

    If you have ArcGIS 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_DEF_ORIG_v2020.py" adds all fields required by the Original Habitat DEF.
    "add_DEF_TRANS_v2020.py" adds all fields required by the Translated Habitat DEF.
    "add_DEF_HD_v2020.py" adds all fields required by the Habitats Directive 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_DEF_ORIG_v2020.py" removes all fields not required by the Original Habitat DEF.
    "trim_DEF_TRANS_v2020.py" removes all fields not required by the Translated Habitat DEF.
    "trim_DEF_HD_v2020.py" removes all fields not required by the Habitats Directive 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.

  • Step 4: Confidence assessment
    File Type Last Modified
    Template: Confidence assessment score sheet .xls 03/04/2015
    Guidance: Confidence assessment .pdf 26/02/2015

    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 assigning a 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.

    Important changes from 2020:

    1. The MESH confidence assessment is no longer an essential requirement for habitat maps submitted to the project, but it should be seen as best practice.
    2. Although the method was designed for assessing habitat maps as a whole, we now accept polygon-level assessments for situations where the confidence varies across a single habitat map.

    Guidance:

    In the Excel template above, 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 or polygon reference in column A. If a confidence assessment can be applied to each polygon, please supply the map GUI and Polygon number to the relevant columns - the PolygonID field will automatically populate. If a confidence assessment can only be applied to the habitat map as a whole, please supply the GUI and leave the Polygon Number column blank.

    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 guidance document (see link above).

  • Step 5: Create a Study Area polygon

    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).

     

    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 shapefile should contain only one feature and must be supplied in the Study Area Data Exchange Format (see step 3 and the Data Exchange Formats page).

    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.

    Automating using Python

    If you have ArcGIS 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.

  • Step 6: Create the metadata
    File Type Last Modified
    Template: INSPIRE-compliant metadata for habitat maps .xml 31/10/2019
    Guidance: Creating INSPIRE-compliant metadata using ArcGIS .pdf 28/11/2019

    For EMODnet Seabed Habitats, metadata is entered into the online habitat mapping metadata catalogue maintained by the International Council for the Exploration of the Seas (ICES).

    You should supply your habitat map’s metadata 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 map viewer can communicate with the metadata catalogue.

    There are many tools available to help you write metadata. To help you, we have created the template and guidance document above.

  • Step 7: Complete the data provider agreement
    File Type Last Modified
    Template: Data Provider Agreement .doc 25/03/2015

    The Data Provider Agreement template 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.

  • Step 8: Submit the data 'package'

    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 (see 'geographical remit'). For any further questions, or queries about the submission process - please contact us.

    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.

     

  • EMODnet Seabed Habitats data provider package