Biosecurity Commons Support Portal

Before you can run any experiment you need to upload or import species occurrence data into the datasets portal. For your climate or environmental data, Biosecurity Commons offers several datasets for you to use. You can also upload your own data for use in your experiments. To import species occurrence data click on “Datasets” and then “Import data”. Under “Please select the data source” click on “Import from third-party”. 

On the next page click on "Species Occurrence". Biosecurity Commons taps into three species data platforms. This is a live feed to the data held on their servers and as such means that you get the most up-to-date data. 

Choose whether you want to search the Atlas of Living Australia (ALA), the Global Biodiversity Information Facility (GBIF) or the Ocean Biogeographic Information System (OBIS) database in the drop-down box.

Note: ALA allows you to search using either a common or Latin name. GBIF and OBIS require you to search using species' Latin names only.

Once you choose a provider, start typing the species name into the search bar and click on "Search provider" on the right-hand side. This will show species related to your search. 

Our Third Party Collaborators 

Atlas of Living Australia (ALA)

• You can view species occurrences on the ALA website by clicking on "View at ALA". Clicking on 'Import' will bring up a pop-up box that gives further options to filter the available data under 'Edit Import options'.

• 'Edit Import options' give a variety of filters like 
  • DOI (Digital Object Identifier) options -  An item or document is permanently identified and linked to on the internet using a string of numbers, characters, and symbols called a digital object identifier (DOI). This option lets users generate and apply DOI to the imported dataset.
  • ALA data assertions – This option helps users check assertions for data records that they wish to remove from the imported dataset. Assertions such as: 
    • Supplied coordinates are zero
    • Basis of record badly formed
    • Coordinate invalid
    • Coordinates centre of the country
    • Coordinates are out of range for species
    • Decimal latitude/longitude conversion failed
    • Supplied coordinates centre of the state
      
  • Basis of records – This option helps users check bases corresponding to the nature of data records that you wish to include in the imported dataset. Bases such as:
    • Fossil specimen
    • Human observation
    • Living specimen
    • Machine observation
    • Material Sample
    • Observation
    • Preserved specimen
    • Unknown

Leaving all options unchecked will disable this filter.

• Geospatial filters – This filter allows users to select specific records with spatial data.
  • Spatial data validity – where the user can choose if required to select data with only valid spatial records or data only with suspected/invalid records.
  • Outlier layer count - where the user can enter the number of environmental spatial layers for which this record has been identified as an outlier by the Reverse Jack-knife method.
  • Coordinate uncertainty – where the user can enter a number for uncertainty in meters (e.g., '25' for 25 meters) to reduce spatial calibration error. 
  • Remove data with duplicate coordinates.
  • Remove data with missing coordinates.
• Time filters  – This filter allows users to refine their data according to year, month, or time of the day.
  • Year – where the user can enter Min and Max number of years.
  • Month – where the user can enter months as a comma-separated list of numbers (e.g. '1,5,11' for January, May, November).
  • Time of day – where the user can enter Min and Max number of days. (Enter time in 24-hour HH:MM: SS format (e.g., '13:45:10' for 1:45:10pm)).

• Miscellaneous filters – This option allows users to filter their data according to the names of record collectors. (Names be entered comma-separated list).

When the filleting is done click 'Import'. You will be redirected to the dataset page with only your datasets, where you can visualise your imported/uploaded dataset. 

Global Biodiversity Information Facility (GBIF)

Once you choose a GBIF, start typing the species name (scientific name) into the search bar and click on "Search GBIF" on the right-hand side. This will show species related to your search.

When the filleting is done click 'Import'. You will be redirected to the dataset page with only your datasets, where you can visualise your imported/uploaded dataset. 

Ocean Biogeographic Information System (OBIS)

Once you choose an OBIS, start typing the species name (scientific name) into the search bar and click on "Search OBIS" on the right-hand side. This will show species related to your search.

When the filleting is done click 'Import'. You will be redirected to the dataset page with only your datasets, where you can visualise your imported/uploaded dataset.