User guide for the Belgian LifeWatch e-Lab | Lifewatch regional portal

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User guide for the Belgian LifeWatch e-Lab

Through this interactive section of the LifeWatch.be portal users can upload their own data using a standard data format, and choose from several web services, models and applications to process the data.

1. HOW TO USE THE WEB SERVICES

2. DESCRIPTION DATA FORMAT

3. DESCRIPTION WEB SERVICES

HowTo


1. HOW TO USE THE WEB SERVICES


1. Upload your file

To upload your own data files to the e-Lab, you will require a log-in and password. You can obtain these freely by registering here.

Note: without log-in and password you can use a marine or terrestrial demo file to discover the functionalities of the e-Lab.

Prepare your data file for upload. Allowed file types: Plain text [TXT], Plain text [CSV], Excel [XLS] and Excel [XLSX]

Note: All web services (except one, see further) require the uploaded data to be in the standard LifeWatch data format, based on and compatible with the OBIS Schema and Darwin Core. In SECTION 2 of this user guide you can find a description of this LifeWatch data format, some examples, and an overview of the required fields for every web service. The only exception is the "Check OBIS file" web service, which requires the uploaded data to be in the OBIS Schema format, instead of the LifeWatch data format.

Click on "Browse" or "Choose file" (depending on your browser) to upload your file. This will open the file explorer on your PC. Select your file.

Heading: use the flag box to indicate whether your first row contains the column names or not.

Column delimiter: select the relevant column delimiter: Tab, Semicolon (;), Comma (,) or Vertical bar (|)

Decimal symbol: select the relevant decimal symbol: Comma (,) or Point (.)

Data format: select "lifewatch" for all web services (except for "Check OBIS file"); only select "obis" for the "Check OBIS file" web service (see above).

 

2. Select web services

Choose the desired web services. Clicking on the "+" next to each category will list the individual web services. In this overview every web service is provided with a short description, source, whether the service is applicable to marine or terrestrial data, and its status. A more extensive description of the web services can be found in SECTION 3 of this user guide.

Services 20140304

 

3. Verify order, change order if necessary and run

The selected web services are shown in the lower part of the screen. In case of multiple web services selected, the order can be changed by dragging the grey bars with the arrows on the left.

 

4. Preview screen

When clicking on "Next", you are redirected to the preview screen. Select the column names from the data format term that correspond to your columns. In the example below a list with coordinates (data file = 2 columns containing latitude and longitude) was uploaded and the requested data service was "Bathymetry Southern Bight of the North Sea". The options "Latitude" and "Longitude" were selected from the data format term.

Preview screen

In the lower section of the preview screen, you can find information about duplicate or missing fields per requested web service.

Duplicate fields can occur in case of concatenated web services: the field is present in the original uploaded data file (the input file), and the field is also generated by a previous web service. Choose the correct field.

 

5. Results

Click "Start". The following message appears:

UC4 - Results

Your results will appear at the top of the results table. The "filename" is the original data file you uploaded. Within the "resultfile" additional columns have been added to the original file, containing information derived from the requested data services. The "resultreport" gives an overview of the requested web services and any errors that might have occurred during the process. These files are linked to your account and can be downloaded for further analysis at any time.

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2. DESCRIPTION DATA FORMAT [Top page]


The LifeWatch.be portal uses a specific standard data format which is based on the OBIS Schema and the Darwin Core Version 2 standard.

This LifeWatch data format is a tab delimited (.txt) ASCII file and can contain the following fields: Survey, LocationID, Longitude, Latitude, WKTFootprint, EventID, SamplingProtocol, EventDate, MinimumDepth, MaximumDepth, FieldNumber, SampleSize, ScientificName, ScientificNameID, Sex, LifeStage, ObservedIndividualCount and AssociatedSequences. An extensive description of each field can be found here.

Not all fields are required for every web service. The table below gives an overview of the required fields for the individual web services:  

Web service category Web service name Required fields in the data format
Data validation and QC services Show on map Latitude, Longitude
Data format validation Latitude, Longitude, EventDate
Check OBIS file  

Marineregions gazetteer services

Get lat-long by mrgid LocationID
Get lat-long by name Location
Get gazetteer name by lat-long Latitude, Longitude
Get lat-long by accepted name Location
Taxon observations Number of observations of a marine taxon ScientificNameID
Number of observations in a 1000m radius around a point Latitude, Longitude
Taxon list of a certain region LocationID
Taxon services Get AphiaID World Register of Marine Species (WoRMS) ScientificName
Reverse taxon match by ITIS TSN ScientificNameID (ITIS TSN)
Reverse taxon match by AphiaID ScientificNameID (AphiaID)
Taxon match ScientificName
Tidal services Calculate tidal reduction Latitude, Longitude, EventDate
Administrative boundaries EMODnet regions Latitude, Longitude
Exclusive Economic Zones (EEZ) Latitude, Longitude
ICES Ecoregions Latitude, Longitude
IHO Sea Areas Latitude, Longitude
Marine Regions (intersect EEZ and IHO) Latitude, Longitude
World Countries Latitude, Longitude
FAO Fishing Areas Latitude, Longitude
Bathymetry Bathymetry Southern Bight of the North Sea Latitude, Longitude
GEBCO bathymetrie Latitude, Longitude
MARSPEC: global marine bathymetrie (Resolution: 30 arc seconds) Latitude, Longitude
Biogeographical classification Longhurst Biogeographical Provinces Latitude, Longitude
Marine Realms of the World Latitude, Longitude
Marine Ecoregions of the World Latitude, Longitude
Marine Provinces of the World Latitude, Longitude
Large Marine Ecosystems of the World Latitude, Longitude
Environmental data Cloud Cover (maximum) Latitude, Longitude
Chlorophyll A (mean) Latitude, Longitude
Chlorophyll A (maximum) Latitude, Longitude
Sea Surface Temperature (maximum) Latitude, Longitude
Silicate (mean) Latitude, Longitude
Diffuse Attenuation (maximum) Latitude, Longitude
Cloud Cover (mean) Latitude, Longitude
Diffuse Attenuation (minimum) Latitude, Longitude
Photosynthetically Available Radiation (mean) Latitude, Longitude
Sea Surface Temperature (mean) Latitude, Longitude
pH (mean) Latitude, Longitude
Photosynthetically Available Radiation (maximum) Latitude, Longitude
Nitrate (mean) Latitude, Longitude
Chlorophyll A (range) Latitude, Longitude
Calcite Concentration (mean) Latitude, Longitude
Cloud Cover (minimum) Latitude, Longitude
Phosphate (mean) Latitude, Longitude
Dissolved Oxygen (mean) Latitude, Longitude
Salinity (mean) Latitude, Longitude
Sea Surface Temperature (range) Latitude, Longitude
Sea Surface Temperature (minimum) Latitude, Longitude
Chlorophyll A (minimum) Latitude, Longitude
Diffuse Attenuation (mean) Latitude, Longitude
Features Shoals (Belgian Continental Shelf) Latitude, Longitude
Protected areas Flemish Ecological Network Latitude, Longitude
Total biological valuation Marine Biological Valuation (Total) Latitude, Longitude
Terrestrial Biological Valuation (v22) Latitude, Longitude

Some example ASCII files can be found here:

[Top page]DataFormat


3. DESCRIPTION WEB SERVICES [Top page]


The web services can also be used in a concatenated way, where the output of the first web service is the input for the next web service. This is demonstrated in the Use cases.

Please note: currently only three concatenated web services are allowed, i.e. currently you can only select 3 web services in 1 job.

Data validation and QC services:

  • Show on map: This service generates a map based on Latitude and Longitude in the uploaded data file. The resulting map is available in the result report.

  • Data format validation: The LifeWatch portal uses a specific standard data format based on Darwin Core and the OBIS Schema (see above). This service checks if the uploaded data file matches this standard LifeWatch data format.

  • Check OBIS file: This service checks if the uploaded data file matches the OBIS Schema (mandatory and missing fields), checks the format of the date and coordinates and checks if the observation points are located at sea or on land. This service also performs a WoRMS taxon match.

Marineregions gazetteer services:

  • Get lat-long by mrgid: Returns the latitude and longitude of the centroid and the preferred gazetteer name of a Marine Regions ID (MRGID), based on the MRGID in the uploaded data file.

  • Get lat-long by name: Returns the latitude, longitude, matched name and the Marine Regions ID (MRGID) of a given gazetteer name in the uploaded data file.

  • Get gazetteer name by lat-long: Returns the Marine Regions place name and the Marine Regions ID (MRGID) of the bounding box (radius 3) based on Latitude and Longitude in the uploaded data file.

  • Get lat-long by accepted name: Returns the latitude, longitude, accepted name and the Marine Regions ID (MRGID) of a given gazetteer name in the uploaded data file.

Taxon observations:

  • Number of observations of a marine taxon: Returns all observation points (latitude and longitude) in the Ocean Biogeographic Information System (OBIS) for a specific species, based on the ScientificNameID in the uploaded data file.

  • Number of observations in a 1000m radius around a point: Returns the number of observations in the Ocean Biogeographic Information System (OBIS) of taxon in a radius of 1000 meter around a point, based on Latitude and Longitude in the uploaded data file.

  • Taxon list of a certain region: Returns a taxon list based on observations from the Ocean Biogeographic Information System (OBIS) for a certain region, based on the Marine Regions ID (MRGID) in the uploaded data file.

Taxon services:

  • Get AphiaID World Register of Marine Species (WoRMS): Returns the (first) exact matching AphiaID for a given taxon name, based on the ScientificName in the uploaded data file.

Tidal services:

  • Calculate tidal reduction: Calculates tidal heights in NAP (Normaal Amsterdams Peil), GLLWS (Gemiddeld Laag LaagWater bij Springtij), and TAW (Tweede Algemene Waterpassing) based on Latitude, Longitude and EventDate in the uploaded data file. The calculations are based on the M2 tidal reduction algorithm and the water levels measured by the monitoring network Flemish Banks.

​​Geographical services - Administrative boundaries:

Geographical services - Bathymetry:

  • ​​GEBCO bathymetrie: returns the bathymetry from the General Bathymetric Chart of the Oceans (GEBCO), based on Latitude and Longitude in the uploaded data file.

  • MARSPEC: global marine bathymetrie (Resolution: 30 arc seconds): Returns the global marine bathymetry with a resolution of 30 arc seconds from the Ocean Climate Layers for Marine Spatial Ecology (MARSPEC), based on Latitude and Longitude in the uploaded data file.

Geographical services - Biogeographical classification:

Geographical services - Environmental data:

  • These web services return environmental data from Bio-ORACLE (Ocean Rasters for Analysis of Climate and Environment): a global environmental dataset for marine species distribution modeling, based on Latitude and Longitude in the uploaded data file. Available parameters include: Sea Surface Temperature (minimum, maximum, mean, range), Salinity (mean), Chlorophyll-a (minimum, maximum, mean, range), Photosynthetically Available Radiation​ (minimum, mean),  pH (mean), Calcite Concentration (mean), Dissolved Oxygen (mean), Silicate (mean), Nitrate (mean), Phosphate (mean), Diffuse Attenuation​ (minimum, maximum, mean), and Cloud Cover (minimum, maximum, mean).

Geographical services - Features:

  • Shoals (Belgian Continental Shelf): Indicates if a given location in the Belgian Continental Shelf is situated on a shoal, based on Latitude and Longitude in the uploaded data file, and gives the name and group of the shoal.

Geographical services - Protected areas:

  • Flemish Ecological Network: Indicates if a given location is situated within the Flemish Ecological Network, based on Latitude and Longitude in the uploaded data file, and gives the type and name of the VEN-area. The Flemish Ecological Network (VEN) is a selection of valuable and sensitive natural areas in Flanders. The Flemish government gives priority to nature conservation and nature development in these areas.

Geographical services - Total biological valuation:

  • Terrestrial Biological Valuation (v22): Returns the terrestrial biological value of a location in the Flemish Region, based on Latitude and Longitude in the uploaded data file and the Biological Valuation Map (version22). The Biological Valuation Map is a uniform field-driven survey of the land cover and vegetation in the Flemish Region.

​​[Top page]DataFormat