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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