1. Upload your file

Select one of the demo data files and choose from several web services, models and applications to process the data.
To work with other data files, please log in.
If you are new to this service, please read the manual.

File

Use demo file: View demo file
Allowed filetypes: Plain text [TXT] | Plain text [CSV] | excel [XLS] | excel [XLSX]
Maximum rows in file:10000

HeadingFirst row contains column names
Column delimiter
Decimal symbol
Data format
  

2. Select webservices

  

3. Verify order, change order if necessary and run

Selected services
Comment:
  uploading file
 
No preview available.

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

Prepare your data file for upload. Allowed file types: Plain text [TXT]. To feed the required information to the portal, you can use the standard LifeWatch data format based on and compatible with Darwin Core and the OBIS Schema. For the web service "Check OBIS file" the data can also be uploaded to the portal in the OBIS Schema format. In Section 2 of the manual you can find a description of the LifeWatch data format, some examples, and an overview of the required fields for every web service. 

Click on "Browse" to upload your file. This will open the file explorer on your PC. Select your file. For uploading your own data files a login and password are required. You can also use a demo file with marine or terrestrial data.

Select the way you have delimited your data by choosing the relevant row and column delimiter. Use the flag box to indicate whether your first row contains the column names or not. Indicate whether you use comma (,) or point (.) as decimal symbol. Select the format the data is in: LifeWatch format or OBIS Schema.

UC1 - Upload your file

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.

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.

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. Check for every web service if the required fields are present in the input file or will be generated by a previous web service.

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 can be downloaded for further analysis at any time.

[Top page]

DataFormat


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 type

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

Taxon services

Taxon match WoRMS

ScientificName

OBIS observations

ScientificNameID

Taxon match

ScientificName

Tidal services

Calculate tidal reduction

Latitude, Longitude, EventDate

Administrative boundaries

World Countries

Latitude, Longitude

ICES Ecoregions

Latitude, Longitude

FAO Fishing Areas

Latitude, Longitude

IHO Sea Areas

Latitude, Longitude

Exclusive Economic Zones

Latitude, Longitude

Bathymetry

Bathymetry Southern Bight of the North Sea

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

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]

WebServices 


3. DESCRIPTION WEB SERVICES [Top page]


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 the Latitude and Longitude in the uploaded data file.

Taxon services:

  • OBIS observations: 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.

Tidal services:

  • Calculate tidal reduction: Calculates tidal heights in NAP, GLLWS, and TAW 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 netword Flemish Banks.

Geographical services - Administrative boundaries:

Geographical services - Bathymetry:

  • This service renders the depth based on Latitude and Longitude in the uploaded data file.

Geographical services - Biogeographical classification:

Geographical services - Features:

  • This service indicates if a given location is situated on a shoal, and is based on Latitude and Longitude in the uploaded data file.

Geographical services - Protected areas:

  • This service indicates if a given location is situated within the Flemish Ecological Network, and is based on Latitude and Longitude in the uploaded data file.

Geographical services - Total biological valuation:

  • These services render both the terrestrial and marine ecological value of a given location, based on Latitude and Longitude in the uploaded data file.

 [Top page]

The LifeWatch web services can be used in a concatenated way, where the output of one web service is the input for another web service. This is demonstrated below in four use cases.

 

Thumbnail Use Case 1   Thumbnail Use Case 2

Thumbnail Use Case 3   Thumbnail Use Case 4

Below you will find a list of previously executed jobs.

Changelog

2014-04-15 added webservice : Get AphiaRecord by ITIS TSN

2014-04-15 added webservice : Reverse taxon match by aphiaID

2014-02-03 added webservice : AfreMAS from http://www.marinespecies.org/afremas/aphia.php?p=searh

2014-01-12 added webservice : check OBIS format

2013-11-26 update : choice possible which taxon match webservices to run

2013-10-24 update : updates to the interface

2013-10-15 changed functionality : Jobqueue added (to be able to limit number of running jobs)

2013-08-13 added function : Choice of input fields

2013-08-05 added function : Concatenate services (Output can be used as input for other services)

2013-08-02 added webservice : getnamebylatlong from marineregions.org

2013-07-16 added webservice : getmrgidbyname from marineregions.org

2013-07-16 added webservice : getlatlongbyname from marineregions.org

2013-07-16 added webservice : getlatlongbymrgid from marineregions.org


USE CASE 1: MARINE SPECIES OBSERVATIONS IN 1000M RADIUS AROUND OBSERVATION POINTS     [demo]


SET UP:

You upload a list with your own marine species observations and want to know how many times these species were already observed in a 1000m radius around your observation points (based on OBIS).

The input file is a text file containing three columns: ScientificName, Latitude, and Longitude (example).

This use case combines two web services in a fixed order: (1) Taxon match, (2) Number of observations in a 1000m radius around a point.

(1) First, the web service 'Taxon match' matches the marine species names to the World Register of Marine Species (WoRMS). If a species name is available in WoRMS, this web service renders its AphiaID (an unique identifier of Aphia, the database behind WoRMS), its status (accepted or unaccepted) and its accepted name. This output information is added as extra columns to the original input file. [NOTE: the taxon match can also match taxon names to other taxonomic databases and nomenclatures, such as e.g. Catalogue of Life (CoL), the Integrated Taxonomic Information System (ITIS), etc. For this use case we only select WoRMS, since the uploaded list contains purely marine species.]

(2) Second, the web service 'Number of observations in a 1000m radius around a point' defines a radius of 1000m around the uploaded observation points. Based on the AphiaID generated by the taxon match, this web service determines the observation records for the species in the Ocean Biogeographic Information System (OBIS), in this specific radius. This number of observations is added to the input file as an extra column.

HOW TO:

1. Upload your file

Upload your data file and select the relevant row and column delimiter and decimal symbol. Select "lifewatch" for data format.

UC1 - Upload your file

2. Select web services

Select the required web services: 'Taxon match' and 'Number of observations in a 1000m radius around a point'.

UC1 - Selected services 

3. Verify order, change order if necessary and run

Only keep 'Taxon match World Register of Marine Species (WoRMS)', remove all other taxon matches. The order of the selected web services can be changed by dragging the grey bars with the arrows. The required web service order for this use case is (1) Taxon match World Register of Marine Species (WoRMS), (2) Number of observations in a 1000m radius around a point.

UC1 - Verify order services

4. Preview screen

When you click "Next", you are redirected to the preview screen. Make sure that every column name from the uploaded file corresponds with a column name from the pick list. In this case choose 'ScientificName', 'Latitude', and 'Longitude'.

UC1 - Preview1

In the lower section of the preview screen, you can find information about duplicate or missing fields per requested web service. Check for every web service if the required fields are present in the input file or will be generated by a previous web service.

UC1 - Preview2  UC1 - Preview3 

5. Results

Click "Start". The following message appears:

UC1 - Results

Click on "Results". Your result file (example) will appear at the top of the results table. The result report gives an overview of the requested web services, the results per web service, any errors that might have occurred during the process, and a legend of the added fields in the result file. The result file is also available through the result report.

UC1 - ResultReport


USE CASE 2: MARINE SPECIES LIST AND NUMBER OF OBSERVATIONS PER GEOGRAPHICAL AREA     [demo]


SET UP:

You upload a list with marine place names (e.g. name of an EEZ, Ocean) and want to know which species have already been observed in these areas, and how many times (based on OBIS).

The input file is a text file containing one column: Location (example).

This use case combines two web services in a fixed order: (1) Get lat-lon by name, (2) Taxon list of a certain region.

(1) First, the web service 'Get lat-lon by name' matches the uploaded place names (e.g. name of an EEZ, Ocean) to the MarineRegions gazetteer, and translates these place names into MRGIDs (Marine Regions Geographic IDentifier). The MRGID is added to the original input file as an extra column. The MRGID can refer to a point location, a polygon or an envelop, but for the next step only polygons and envelops are taken into account.

(2) Second, the web service 'Taxon list of a certain region' generates a marine species list derived from the Ocean Biogeographic Information System (OBIS) for this MRGID. The ScientificName and AphiaID (the unique identifier of the World Register of Marine Species - WoRMS) are added to the original input file as extra columns.

HOW TO:

1. Upload your file

Upload your data file and select the relevant row and column delimiter and decimal symbol. Select "lifewatch" for data format.

UC2 - Upload your file

2. Select web services

Select the required web services: 'Get lat-lon by name' and 'Taxon list of a certain region'.

UC2 - Selected services

3. Verify order, change order if necessary and run

The order of the selected web services can be changed by dragging the grey bars with the arrows. The required web service order for this use case is (1) Get lat-lon by name, (2) Taxon list of a certain region.

UC2 - Verify order services

4. Preview screen

When you click "Next", you are redirected to the preview screen. Make sure that every column name from the uploaded file corresponds with a column name from the pick list. In this case choose 'Location'.

UC2 - Preview1

In the lower section of the preview screen, you can find information about duplicate or missing fields per requested web service. Check for every web service if the required fields are present in the input file or will be generated by a previous web service.

UC2 - Preview2   UC2 - Preview3

5. Results

Click "Start". The following message appears:

UC2 - Results

Click on "Results". Your result file (example) will appear at the top of the results table. The result report gives an overview of the requested web services, the results per web service, any errors that might have occurred during the process, and a legend of the added fields in the result file. The result file is also available through the result report.

UC2 - Resultreport


USE CASE 3: LIST OF GEOGRAPHICAL AREAS PER MARINE SPECIES     [demo]


SET UP:

You upload a list of marine species names and want to know in which Exclusive Economic Zones (EEZs) these species have already been observed (based on OBIS).

The input file is a text file containing one column: ScientificName (example).

This use case combines three web services in a fixed order: (1) Taxon match, (2) Number of observations of a marine taxon, (3) Exclusive Economic Zones.

(1) First, the web service 'Taxon match' matches the marine species names to the World Register of Marine Species (WoRMS). If a species name is available in WoRMS, this web service renders its AphiaID (an unique identifier of Aphia, the database behind WoRMS), its status (accepted or unaccepted) and its accepted name. This output information is added to the original input file as extra columns. [NOTE: the taxon match can also match taxon names to other taxonomic databases and nomenclatures, such as e.g. Catalogue of Life (CoL), the Integrated Taxonomic Information System (ITIS), etc. For this use case we only select WoRMS, since the uploaded list contains purely marine species.]

(2) Second, the web service 'Number of observations of a marine taxon' determines the observation records for the species in the Ocean Biogeographic Information System (OBIS). For this, the web service uses the AphiaID, the output of the taxon match. Every OBIS observation record is characterized by a cs_code, which is translated into coordinates. The cs_code, latitude and longitude are added as extra columns to the original file.

(3) Third, the web service 'Exclusive Economic Zones' determines in which EEZs these coordinates are located. The name and MRGID (Marine Regions Geographic Identifier) of the EEZs are added to the input file as extra columns. [NOTE: if you are not interested in EEZs, you can also choose other geographical areas, such as IHO Sea Areas, Longhurst Biogeographical Provinces, etc.]

HOW TO:

1. Upload your file

Upload your data file and select the relevant row and column delimiter and decimal symbol. Select "lifewatch" for data format.

UC3 - Upload your file

2. Select web services

Select the required web services: 'Taxon match', 'Number of observations of a marine taxon', and 'Exclusive Economic Zones'. [Note: if you are not interested in EEZs, choose another geographical area, e.g. IHO Sea Areas, Longhurst Biogeographical Provinces, etc.]

UC3 - Selected services

3. Verify order, change order if necessary and run

Only keep 'Taxon match World Register of Marine Species (WoRMS)', remove the other taxon matches. The order of the selected web services can be changed by dragging the grey bars with the arrows. The required web service order for this use case is (1) Taxon match World Register of Marine Species (WoRMS), (2) Number of observations of a marine taxon, (3) Exclusive Economic Zones.

UC3 - Verify order services

4. Preview screen

When you click "Next", you are redirected to the preview screen. Make sure that every column name from the uploaded file corresponds with a column name from the pick list. In this case choose 'ScientificName'.

UC3 - Preview 1

In the lower section of the preview screen, you can find information about duplicate or missing fields per requested web service. Check for every web service if the required fields are present in the input file or will be generated by a previous web service.

UC3 - Preview2UC3 - Preview3UC3 - Preview4

5. Results

Click "Start". The following message appears:

UC3 - Results

Click on "Results". Your result file (example) will appear at the top of the results table. The result report gives an overview of the requested web services, the results per web service, any errors that might have occurred during the process, and a legend of the added fields in the result file. The result file is also available through the result report.

UC3 - Result report


USE CASE 4: QUALITY CONTROL OF BIODIVERSITY DATA SETS     [demo]


SET UP:

You upload an entire data set and want to perform a series of quality control steps on your data.

The uploaded data set needs to be in a certain data format. Several formats are currently available: the Darwin Core, the OBIS scheme and the LifeWatch data format. The Darwin Core is a standard that is used by the Global Biodiversity Information Facility (GBIF) and others. The OBIS scheme was built as an extension of the Darwin Core version 2. The LifeWatch data format was developed specifically for the LifeWatch.be portal and is based on both the Darwin Core and the OBIS scheme. More detailed information about the LifeWatch data format can be read in the manual.

If the dataset is formatted in the OBIS scheme, you can choose the web service 'Check OBIS file'. This web service checks which mandatory fields are present or missing, and checks if values are missing in the mandatory fields. This web service also generates a map and validates the coordinates (sea-land) and the dates. Furthermore, this web service performs a taxon match with the World Register of Marine Species (WoRMS).

If the dataset is in the LifeWatch data format, you can choose the web service 'Data format validation'. This web service checks which fields do not belong to the data format, and validates the values in the fields longitude, latitude and eventdate. To further validate the content of the data set, you can choose additional data services. First, you can perform a taxonomic quality control through the web service 'Taxon match'. This web service checks if the uploaded taxon names are recorded in existing taxonomic databases and nomenclatures such as the World Register of Marine Species (WoRMS), the Catalogue of Life (CoL), the Integrated Taxonomic Information System (ITIS), Index Fungorum (IF), the International Plant Names Index (IPNI), the Global Names Index (GNI), the Paleobiology Database (Paleo), and the Pan-European Species directories Infrastructure (PESI). If a taxon name is available in these databases, this web service renders, for each database, its ID, its status (accepted or unaccepted) and its accepted name. The web service can match the uploaded taxon names to all taxonomic databases at once or to a selection. For instance, if the dataset contains purely marine taxa, you can select Taxon match World Register of Marine Species (WoRMS) and remove the other taxon matches. Second, you can perform a geographic quality control, i.e. check the coordinates, through the web service 'Show on map'. The output of this web service is a map with the plotted coordinates. Here you can verify very quickly if marine observation points are indeed plotted in marine areas, and terrestrial observation points are indeed plotted on land.

For this use case the order of the selected web services is not relevant. The 'Check OBIS file' web service needs to be performed separately, since the input file for this web service is a dataset in the OBIS scheme (example). The 'Data format validation', 'Taxon match' and 'Show on map' web services can be performed simultaneously. The input file for these web services is a dataset in the LifeWatch data format (example).

HOW TO:

1. Upload your file

Upload your data file and select the relevant row and column delimiter and decimal symbol. Select the data format: OBIS scheme for 'Check OBIS file' and LifeWatch data format for 'Data format validation', 'Taxon match' and 'Show on map'.

UC4 - Upload your file

2. Select web services

Select the required web services: 'Check OBIS file' (OBIS scheme format).

UC4 - Selected services OBIS

Select the required web services: 'Data format validation', 'Taxon match' and 'Show on Map' (LifeWatch data format).

UC4 - Selected services LifeWatch

3. Verify order, change order if necessary and run

For this use case the order of the selected web services is not relevant.

4. Preview screen

When you click "Next", you are redirected to the preview screen. Make sure that every column name from the uploaded file corresponds with a column name from the pick list.

For web service 'Check OBIS file':

UC4 - Preview screen OBIS

For web services 'Data format validation', 'Show on map' and 'Taxon match WoRMS':

UC4 - Preview screen LW

In the lower section of the preview screen, you can find information about duplicate or missing fields per requested web service. Check for every web service if the required fields are present in the input file or will be generated by a previous web service.

5. Results

Click "Start". The following message appears:

UC4 - Results

Click on "Results". Your result file will appear at the top of the results table (example for OBIS scheme format, example for LifeWatch data format). The result report gives an overview of the requested web services, the results per web service, any errors that might have occurred during the process, and a legend of the added fields in the result file. The result file is also available through the result report.

Result report for web service 'Check OBIS file':

UC4 - ResultReport

Result report for web services 'Data format validation', 'Show on map' and 'Taxon match WoRMS':

UC4 - ResultReport LW