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.]
1. Upload your file
Upload your data file and select the relevant row and column delimiter and decimal symbol. Select "lifewatch" for data format.
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.]
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.
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'.
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.
Click "Start". The following message appears:
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.