We have replaced the concept of an assemblage with Lists. A list, like the assemblage, is any combination of species but we have now formalized the generation, management and use of these lists. They key difference between the assemblage and the lists is that Lists are retained by the system for future use.
To use the full functionality of Lists, you must register on the Atlas site as the List is stored against your name. Lists are by default public but as a List owner, they can be restricted or deleted after use.
A List can be created on the fly in the Spatial Portal or through the Lists page. You can share administrative functions with other registered ALA users: Lists can be edited by anyone given the authority. Taxa can be added, modified or deleted from the List and the List can be deleted if no longer required.
NOTE: Lists created via the Spatial Portal (on the fly) are by default created as PRIVATE lists. This means that they will not be exposed on http://lists.ala.org.au. These private lists can be edited and shared using the Lists functionality. You can choose to make your list publicly accessible when creating it or later. If the list is temporary, please remove it once the project or exercise has been completed.
A List can be used anywhere the spatial portal asks for species (or other taxa) input. The options when inputting taxa are:
- All species
- Search for a species by scientific or common name
- Create a new List of species
- Use an existing List of species
- Upload points
The following example shows adding a species layer to the map, with the option to create an on the fly list selected.
Select Add to map | Species, Create new species list.
A species List is a group of taxa/species. The Spatial Portal can create this list and generate one mapped layer that can be be used in the same way as a single species layer. For example, faceting, filtering, scatterplots, prediction, points to grid, GDM and exports.
Create a Species List
A species List can be created on the fly by typing or pasting in any combination of scientific or common names or LSIDs (Life Science Identifiers) into the species selection multi-line text box and clicking the Add button.
After clicking the Add button, a list will be generated in the Species list section:
The names or IDs will be looked up in the National Species List and you can see in the list whether the names are found as the family, kingdom and count columns will be populated. The look up accepts synonyms and will match on currently accepted names. If a species name does not exist in the National Species List, but the genus does, then it will create a match against the whole genera. Unmatched names will also be listed.
The names or IDs will be looked in the National Species List. The look up accepts synonyms and will match on currently accepted names. If a species name does not exist in the National Species List, but the genus does, then it will create a match against the whole genera.
The returned records list of scientific names, includes those that are found and not found. If a match can't be found, there is the option to search for a match.
Press the click to search in the family column for unmatched species. This will copy the species into the Add from search text field. This uses a different search system using auto-complete. It is usually effective to remove a few letters to search for close names. Hover over the taxon you require and click it once it highlights. It will be added to the species list below.
Building a list via the search box
You can build a List by using the Add from search text field to add scientific names or common names, one by one. Common names found to be ambiguous, like Brown snake in the example below, will be display the scientific names associated with the common names to allow you to select the correct taxon.
Once you have entered all the taxa you require into the list, click the Next button.
You will be asked to name your list and you have the option to give it a description. By default, the list will be Private, but can be made a public list by clicking the checkbox to remove the tick.
Use an Existing Species List
If a List has been previously created, it can be used wherever a single species/taxa can be used. The List may have been created by you or by another registered user. When you select Use existing species list, the list of Lists is displayed and one or more Lists can be selected for use. You can use the filter option to help find a specific list.
As noted above, regardless of the number of taxa, the List will be mapped as a single species layer with all associated occurrence records. You can subsequently facet the mapped layer on scientific name or a host of other features. This will display the classes of the facet as separate colour on the map. You can also create a new layer by filtering on a subset of classes of the facet.
Restrict to an Area
The options in the Restrict to an area section limits the mapping of occurrence records to an area. Areas may be:
- mapped in the spatial portal prior to adding the species occurrence
- selected from system defaults of current extent, Australia, and the world
- selected on the fly via the Define new area... option.
Any areas already defined on the map will be available.
Defining a new area allows you to add an area layer using any one of 14 options.
The figures below are examples of mapping multiple species by the use of Lists.
1. Occurrences added to a map via a list.
2. Occurrences added to a map via and list and faceted on scientific name.
3. Occurrences added to a map via a list and displayed as a density grid
Add the species list to the map, then click on the option Density grid.
Selecting Density grid changes the map to display the species occurrences in one degree density grids. If the number of occurrences to be displayed on the map are 100,000 or over, then the map defaults to the density grid.
The legend show the species assemblage occurrence counts, e.g. 0 to 99, 100 to 199.
When the layer metadata icon icon is selected in the layers list for the species assemblage the metadata is displayed.
Demonstration Youtube Video
Note: this demo uses an older version of the spatial portal, however all functions for mapping multiple species are still available.
By Lee Belbin, Geospatial Team Leader