The Atlas has changed its methods for keeping you informed about significant developments.

  • We now have a means where you can receive email alerts about new blog posts on the website with a choice of frequencies. This replaces the previous quarterly e-newsletter.
  • We have an RSS feed that broadcasts all new blog posts.
  • We have a Twitter account that lets you follow incidental Atlas’ stories.

To view all blog updates, click here »

If you previously subscribed to receive the newsletter, we have created an Atlas account for you to receive Atlas blog posts on a monthly basis. You can opt out altogether or change the frequency!

If you wish to have your account deleted and receive no blog post email notifications, please email info@ala.org.au

How to set your blog email alerts

MyProfile & Login in the header

MyProfile & Login in the header

Click the My profile link in the header, then Manage email alerts about new items added to the Atlas. (See images below).

(If you have not logged in you will be initially redirected to the Login page, where you will need to type your registered email and password).

Users without a pre-existing Atlas account

For those of you who asked to receive a newsletter (generally prior to April 2011), but did not have a pre-existing Atlas account – we have created a default account for you – to receive monthly blog posting updates from the Atlas.

Read about details of your default account and resetting your password »

Subscribe to newsletter

Click to see Full Edit Profile

Users with a pre-existing Atlas account

If you had asked to subscribe to the Newsletter in your My Profile, then we’ve changed your account to receive monthly blog posting update alerts from the Atlas.

If you did NOT subscribe to the Newsletter, then we have not set any alerts. However, you might consider signing up for them.

Email Alerts

It is as simple as clicking on Manage email alerts, choosing the frequency in the pull down list and clicking on the alert buttons you require to ‘Enabled’ or ‘Disabled’.

Email alerts

Email alerts - more than just blog posting alerts

Email Alerts change the frequency

Email Alerts change the frequency by the pull down frequency list

Email alerts disable

Email alerts are disabled by clicking on the disable button

The Atlas has changed its methods for keeping you informed about significant developments via regular blog news postings, RSS and a Twitter account.

The quarterly e-newsletter has been discontinued and replaced with regular blog news items posted on our site. To be alerted about these posts via email you need a My Profile account on the Atlas site.

If you previously subscribed to receive the e-newsletter (generally prior to April 2011) and did not have an Atlas account, we have created one for you in order to send you new Atlas blog postings on a monthly basis. You can opt out altogether or change the frequency.

An Atlas My Profile account allows you to contribute sightings and images to the Atlas, track sessions within the Spatial Portal and ask to be alerted of any new additions to the Atlas, including Atlas blog news postings.

Once you have logged in, you can alter the frequency or enable/disable your blog posting alerts. Read how »

If you wish to have your account deleted and receive no blog post email notifications, please email info@ala.org.au


Default Atlas accounts

In all the headers is a ‘My profile’ and ‘Log in’ (or ‘Log out’) link. Click the Log in link.

MyProfile & Login in the header

MyProfile & Login in the header

The email you registered with us for the Atlas newsletter is the email to use for your Atlas login. Your default Password has been assigned based on the name portion of your email address. That is the characters before the ‘@’ in your email address. If your email name portion is shorter than six characters you will need to repeat your full email name portion, until your password exceeds six characters.

We ask that you reset your password from the default one we provided.

Some Email and Default Password Examples:

Example Login Screen

Example Login Screen - Password would normally be obscured

Email Password Comments
john.doe@gmail.com john.doe Greater than 6 chars, use all email name
martin@yahoo.com martin Exactly 6 chars, use all email name
alan@gmail.com alanalan Less than 6 chars, repeat email name until >= 6 chars
jo@yahoo.com jojojo Less than 6 chars, repeat email name until >= 6 chars

How to reset my password

The Login page has a link to Reset Your Password.

Reset Your Password

Reset Your Password

Pressing the ‘Send Password Reset Link’ button will send you a link to your email address allowing you to enter a new password. There is a time limit of 48 hours.

Article

'FieldData software' – citizen science training course

The Atlas of Living Australia recently held a successful three day training workshop for a group of current and new users in the use of its FieldData software. This online software (also known as the Biological Data Recording System, BDRS) was developed in collaboration with Gaia Resources and is being made available to a broad range of citizen science groups to collect and manage their field-captured data as well as share their information with others through the Atlas. The course was convened and run by project managers Owen Butler and Peter Brenton from the Atlas, with other guest speakers from the Atlas and users of the FieldData software. Attendees represented a wide range of organisations and interests with 30 participants representing 15 organisations, including NGOs, local Catchment Management Authorities, several community naturalist groups and research groups within CSIRO. Participants came from as far away as Townsville and Perth to learn how to use the online open source Atlas tools to manage their field data, and join a growing community of users, plus get the opportunity to enjoy this year’s glorious Canberra summer weather! FieldData Training Course: Day 1 – Basic Administration of the FieldData software, Day 2 – Advanced, Day 3 – For Developers.
FieldData Training Course.

Participants at the FieldData Training Course, February 2012.
Photo courtesy: Robyn Lawrence, Atlas of Living Australia.

The course featured slides and talks, live demonstrations of the site and hands-on practise in setting up ‘mock-up’ versions of the FieldData portal for entry of ad-hoc and survey material. The course material covered:
  • Where the FieldData software fits into the Atlas infrastructure
  • How this set of integrated tools can be used to help meet your organisational field data capture, information management and community support goals
  • Using the software:
    • Understanding how your requirements can be met using the software
    • Setting up a FieldData site for your organisation
    • Registering and managing users
    • Creating field guides and profiles for species of interest in your local area
    • Creating survey and activity tracking forms to log sightings and other information
    • Uploading existing data into your site
    • Viewing your data online in your site and in the Atlas itself (Great Eastern Ranges regions example)
    • Downloading data for further analysis and reporting in other tools
  • How to add your own look and feel to the site – theming
  • Futures – where we can go together from here
The course concluded with a short excursion by the Fungimap participants to photograph a colony of Deathcap mushrooms. More on the recent outbreak of Deathcap mushrooms in Canberra »

Using the FieldCapture tool in the great outdooors

It was especially interesting to learn about the attendees wide-ranging plans for using the FieldData tool to meet diverse needs. Its not just about recording sightings of birds, frogs, plants, fungi … Current portal projects – Feb 2012 (PDF 59KB)
Marine debris found in Mallacoota, Victoria.

Marine debris found in Mallacoota, Victoria.
Photo courtesy: Genevieve Perkins, CSIRO

The TeachWild group sponsored by Shell, Earthwatch Australia and CSIRO is using the FieldData tool to track marine debris – which includes plastics, fishing lines, you name it – junk that is not meant to be in our marine environment – as well as tracking coastal and marine wildlife.

“All the data collected is included on a national debris map overlaid with wildlife distribution patterns for marine species such as birds, fish and turtles, allowing researchers to pinpoint the type of rubbish most dangerous to particular species”.

Dr Denise Hardesty, TeachWild

Read about the recent launch of the TeachWild Marine Debris portal in schools » The Atlas of Life in the Coastal Wilderness (ALCW) is also about to put the FieldCapture tool through its paces. On the 30 and 31 of March 2012, the ALCW is holding a ‘Bioblitz’ for recording as much biological data as they can possibly find over a period of two days in sites around coastal Bermagui in New South Wales. Learn more about the ALCW and join the upcoming Bioblitz » CSIRO researchers are also using the FieldData tool to involve the community across the range of Yellow Box (Eucalyptus melliodora) to collect seed and record information about seed trees and their local environment for a species resilience study. This is involving the non-science community in significant real scientific research work. Several natural resource management (NRM) groups are also using the FieldData tool for recording their various group activities including community events and on-ground works. This will enable them to better track and manage their activities and report on activities and outcomes far more easily and accurately than has ever been possible before.

The Atlas of Living Australia recently held a successful three day training workshop for a group of current and new users in the use of its FieldData software.

This online software (also known as the Biological Data Recording System, BDRS) was developed in collaboration with Gaia Resources and is being made available to a broad range of citizen science groups to collect and manage their field-captured data as well as share their information with others through the Atlas.

The course was convened and run by project managers Owen Butler and Peter Brenton from the Atlas, with other guest speakers from the Atlas and users of the FieldData software.

Attendees represented a wide range of organisations and interests with 30 participants representing 15 organisations, including NGOs, local Catchment Management Authorities, several community naturalist groups and research groups within CSIRO.

Participants came from as far away as Townsville and Perth to learn how to use the online open source Atlas tools to manage their field data, and join a growing community of users, plus get the opportunity to enjoy this year’s glorious Canberra summer weather!

FieldData Training Course:

Day 1 – Basic Administration of the FieldData software, Day 2 – Advanced, Day 3 – For Developers.

FieldData Training Course.

Participants at the FieldData Training Course, February 2012.
Photo courtesy: Robyn Lawrence, Atlas of Living Australia.

The course featured slides and talks, live demonstrations of the site and hands-on practise in setting up ‘mock-up’ versions of the FieldData portal for entry of ad-hoc and survey material.

The course material covered:

  • Where the FieldData software fits into the Atlas infrastructure
  • How this set of integrated tools can be used to help meet your organisational field data capture, information management and community support goals
  • Using the software:
    • Understanding how your requirements can be met using the software
    • Setting up a FieldData site for your organisation
    • Registering and managing users
    • Creating field guides and profiles for species of interest in your local area
    • Creating survey and activity tracking forms to log sightings and other information
    • Uploading existing data into your site
    • Viewing your data online in your site and in the Atlas itself (Great Eastern Ranges regions example)
    • Downloading data for further analysis and reporting in other tools
  • How to add your own look and feel to the site – theming
  • Futures – where we can go together from here

The course concluded with a short excursion by the Fungimap participants to photograph a colony of Deathcap mushrooms.
More on the recent outbreak of Deathcap mushrooms in Canberra »

Using the FieldCapture tool in the great outdooors

It was especially interesting to learn about the attendees wide-ranging plans for using the FieldData tool to meet diverse needs.

Its not just about recording sightings of birds, frogs, plants, fungi … Current portal projects – Feb 2012 (PDF 59KB)

Marine debris found in Mallacoota, Victoria.

Marine debris found in Mallacoota, Victoria.
Photo courtesy: Genevieve Perkins, CSIRO

The TeachWild group sponsored by Shell, Earthwatch Australia and CSIRO is using the FieldData tool to track marine debris – which includes plastics, fishing lines, you name it – junk that is not meant to be in our marine environment – as well as tracking coastal and marine wildlife.

“All the data collected is included on a national debris map overlaid with wildlife distribution patterns for marine species such as birds, fish and turtles, allowing researchers to pinpoint the type of rubbish most dangerous to particular species”.

Dr Denise Hardesty, TeachWild

Read about the recent launch of the TeachWild Marine Debris portal in schools »

The Atlas of Life in the Coastal Wilderness (ALCW) is also about to put the FieldCapture tool through its paces. On the 30 and 31 of March 2012, the ALCW is holding a ‘Bioblitz’ for recording as much biological data as they can possibly find over a period of two days in sites around coastal Bermagui in New South Wales. Learn more about the ALCW and join the upcoming Bioblitz »

CSIRO researchers are also using the FieldData tool to involve the community across the range of Yellow Box (Eucalyptus melliodora) to collect seed and record information about seed trees and their local environment for a species resilience study. This is involving the non-science community in significant real scientific research work.

Several natural resource management (NRM) groups are also using the FieldData tool for recording their various group activities including community events and on-ground works. This will enable them to better track and manage their activities and report on activities and outcomes far more easily and accurately than has ever been possible before.

Searching the Atlas

There are two main ways to search the Atlas:

  1. Regular searching of the Atlas (non-occurrence records) – species information pages, data sets, Atlas static HTML site pages
  2. Search for occurrences records – sightings, specimens, molecular data, images, conservation & sensitive species statuses

In addition, there is a separate subset searching method of 1. Regular searching, for searching Data sets only.

Where to find these search methods

On the Home page. ‘Search the Atlas’ is prominently displayed at the top of the page below the header, and on all other pages as a search field in the header, e.g. on the Blogs & News page. Both ‘Search the Atlas’ methods look for non-occurrence records.

Search the Atlas on the Home Page

'Search the Atlas' on the Home Page

Search the Atlas search field

'Search the Atlas' search field on non-home pages

On the Data sets page, found by clicking the Data sets icon on the home page. Search for occurrences records is on the left, and search for Data sets only is on the right.
 

Buttons on the home page

Buttons on the home page

Data sets page

Data sets page


Regular searching the Atlas

To ‘Search the Atlas’ for all non-occurrence records, not just data sets (as mentioned above), conduct a search on the home page, or in the search field in the header of every page except the home page.

Search the Atlas for species information

In the home page of the Atlas, search the Atlas for species information


 
Search the Atlas for the data set EMBL

In the home page of the Atlas, search the Atlas for data sets, in this case 'EMBL'.

To reiterate, the ALA home page search, searches the ALA Word Press static HTML pages, all data sets, and species information pages. It does not search for individual occurrence records – sightings, specimens, molecular data, images, conservation & sensitive species statuses – but does find the name and acronym of the data sets holding such records.
 

Search the Atlas search field

Search the Atlas search field

The ‘Search the Atlas’ search field at the top of every non-home page does the same thing.

More detail to be added later »

Searching for occurrence data in the Atlas

To search for individual occurrence records (as mentioned above), click on the ‘Data sets‘ button on the home page. Then click on the ‘Search for occurrences records’ to the left of the page. See image above.

More detail to be added later »

Searching for data sets in the Atlas

Data sets hold digitised occurrence records. They represent many different types of record (as mentioned above).

To search for data sets, click on the ‘Data sets’ button on the home page. Then click on the ‘View data sets’ to the right of the page. See images above.

Data sets searched for EMBL

Results of searching for the data set, 'EMBL'

Click the Data set name e.g., European Molecular Biology Laboratory Australian Mirror, to access the metadata resource page about the data set.

Click the View records to access all occurrence records for the particular data set, in this case the 100,000+ records of ‘EMBL’. See image below.

Regular search results for a data set, in this case EMBL

Regular search results for a data set, in this case EMBL

Or as mentioned above, type in the data set acronym or name into the home page search field, or into the search field in the header in every non-home page.

A result set is returned. It includes the Data set for ‘European Molecular Biology Laboratory Australian Mirror’, plus other records matching the seach term – ‘EMBL’.

Click the Data set name e.g., European Molecular Biology Laboratory Australian Mirror, to access the metadata resource page about the data set.

The user is taken to the Data set resource page for EMBL.

The user is taken to the Data set resource page for 'EMBL'.

The user is taken to the Data set resource page for the ‘European Molecular Biology Laboratory Australian Mirror’ (EMBL). Scroll down the page to find the Map of records, and the link to ‘Click to view records for the European Molecular Biology Laboratory Australian Mirror resource‘.
 

Occurrence results for the data set, EMBL

Occurrence results for the data set, 'EMBL'

All the occurrence records are displayed for the Data set.

Note: Another way to find to all occurrence records for a data set, is to use the Occurrence record search, but to type in the full name of the data set, in this case ‘European Molecular Biology Laboratory Australian Mirror‘. Typing the acronym will not work, as the occurrence records hold only the full data set name.

More detail to be added later »

How to find Molecular Data

The linked example, Search for Molecular Data, demonstrates how to look for known data sets that contain genetic material.

Plus it shows how to facet the occurrence searches for molecular data, then download the data.

And better still, use the Spatial Portal in a simple yet powerful way to search for molecular data, visually display the records, and download the results.

The following applies for searching any data set in the Atlas, using facets to restrict the occurrence search result set, for querying the Spatial Portal, and for downloading.

We will choose a particular data set, filter (facet) on a particular type of record – in this case those with molecular DNA data, and look for a particular group of organisms.

Of course, you can experiment with your own searches, faceting and downloads …

How to search the Atlas

For general information on how to search the Atlas »

How to search for Data sets

If you are interested in a particular data set, for instance those containing molecular data e.g., the ‘European Molecular Biology Laboratory Australian Mirror’ or ‘BOLD – Australia’, then one way to access their records is to find the data set, view and then optionally download the associated occurrence records.

Currently, only one data set in the Atlas holds records with DNA samples, with a record type of ‘GenomicDNA’. The data set is the ‘European Molecular Biology Laboratory Australian Mirror’, with an acronym of ‘EMBL‘. Read how to search for data sets »

Note: The ‘BOLD – Australia’, (acronym = ‘BOLD’) data set holds molecular data, but currently its record type is set to ‘PreservedSpecimen’ not ‘GenomicDNA’. It is hoped this anomaly will be addressed before long.

Or you could facet (filter) the results of an occurrence search for molecular data, and download the records. Read more »

Or better yet, use the Spatial Portal to search for molecular data, visually display the records, and download the results. Read more »

With the downloaded results you can access other external molecular tools. Read more »


Facet the results of an occurrence search

On the occurrence search page, the search text field matches against any attribute of an occurrence record e.g., scientific name (at any taxonomic level), collector, data set full name etc.

Search the occurrence records for Lepidoptera

Search the occurrence records for Lepidoptera

In the following detailed example, we match against the order, Lepidoptera, by typing it in the auto-complete Search field.

We facet (filter) the record by clicking the Record Type – ‘GenomicDNA’ – to restrict the selection to only those Lepidopteran records with molecular DNA data. Currently, this data only is available in the EMBL data set, so the ‘European Molecular Biology Laboratory Australian Mirror’ is the only Dataset shown in the available facets list to the left.
 

Lepidopteran occurrence results faceted for genomic data

Lepidopteran occurrence results faceted for genomic data

The user can further facet the returned results to the user’s specific area of interest by clicking on additional facet class values – note only one per facet, e.g. choose a State/Territory.

Pressing the ‘Downloads’ button, brings up dialogue window for the user to fill in their details. A zip file of occurrence records (data.csv) and a list of data providers (citations.csv) is produced by pressing ‘Download All Records’. See Downloading »

When viewing a list of occurrence records from the EMBL data set – accessed by many means – navigate to an individual record by clicking the on the link View record.

A single occurrence record from the data set EMBL

Example of an individual Occurrence record from the data set 'EMBL'.

Using an individual occurrence record to access the European Nucleotide Archive (ENA)

For ‘European Molecular Biology Laboratory Australian Mirror’ records, click on the More details link. You will be taken to an individual EMBL record in the European Nucleotide Archive.

EMBL occurrence data record displayed through the European Nucleotide Archive (ENA)

EMBL occurrence data record displayed through the European Nucleotide Archive (ENA).

EMBL has a significant tool set to capture and manipulate sequence data.

When on the occurrence record results page, clicking the ‘Map’ tab produces a basic overview map of the points (see image below). Some additional faceting by colours is available on the map under ‘Colour by’ and the ‘Legend’.

Clicking on the map tab displays a basic map of the Lepidopteran points with molecular DNA data.

Clicking on the map tab displays a basic map of the Lepidopteran points with molecular DNA data.

Clicking on the View in spatial portal sends the same query to the Spatial Portal – a powerful and interactive mapping and analysis tool. See Spatial Portal Help »

The Spatial portal displaying molecular occurrence data for the Order Lepidoptera.

The Spatial portal displaying molecular occurrence data for the Order Lepidoptera, with an additional area added to the map.

Catalogue Numbers can be used to download selected sequences either individually or in groups from the EMBL source site. The ability to select just the sequence data from targeted areas or from any facet division meaningful to the user, provides a powerful way of targeting only the pertinent sequence data for download.

In the image above, an area around Forbes has been added. The user can choose to selectively download only those records within the area. See Spatial Portal Add Areas to Map and Export Point Sample »
 
The Catalogue Numbers of the occurrence records can be extracted from the download (data.csv) and used to create a simple comma delimited file which can be uploaded into the ENA search screen. (There are multiple ways this site can accept input search queries).

Test txt file of Catalogue Numbers

Test txt file of Catalogue Numbers for loading into other external tools

In the ENA, click on ‘Choose File’ and browse to find a file containing Catalogue Numbers, ‘test.txt’ in the above image.

Add the text file with Catalogue Numbers in ENA

Add the text file with Catalogue Numbers in ENA

EMBL occurrence data record displayed through the European Nucleotide Archive (ENA)

EMBL occurrence data record displayed through the European Nucleotide Archive (ENA)

Results from the search can then be downloaded into multiple formats including, Text, XML or FASTA.
A similar process is also available through the NCBI nucleotide repository.

Data imported into the alignment package (BioEdit) using the FASTA file download option.

BioEdit Sequence Alignment Editor

BioEdit Sequence Alignment Editor

Use the Spatial Portal to facet the results for Genomic Lepidopteran data for an area

The same process described above using the Atlas to search for data sets, view and download occurrence records containing genomic data can be ‘replicated‘ using the Spatial Portal. For more info »

Useful Links

  • A Blog post about Molecular Data through the ALA’s Data sets and the Spatial Portal. Read more »

By Sapphire McMullan-Fisher, ALA Fungimap Project Manager

The recent wet summer in Canberra led to tragic consequences when a meal mistakenly containing Deathcap mushrooms was eaten:

Deathcaps in Canberra parklands

Deathcap mushrooms (Amanita phalloides) found under Pin Oaks (Quercus palustris).
Photo courtesy: Robyn Lawrence

More information about Deathcap mushrooms can be found at the Australian National Botanic Gardens Deathcap page and the Atlas’ species information page »

Eating any mushrooms found in the wild is not recommended unless you are highly knowledgeable about local poisonous and edible mushrooms.

Some Australian mushrooms and other fungi look similar to edible species from overseas but may be highly poisonous.

Agaricus sp. found in local Canberra parkland. Edibility unknown.

Agaricus sp. found in local Canberra parkland.
Edibility unknown.
Photo courtesy: Sapphire McMullan-Fisher.

 
The button and field mushrooms we buy from shops and markets belong to a genus called Agaricus. There are many species of Agaricus, some may be edible and others are not. Whether edible or not, these mushrooms can appear in our local gardens, parklands and bush areas, and do part of the important job of decomposing in our local areas.

Many fungi have the job of decomposing things which die. Think of the leaves and twigs that fall from trees, and lie around before eventually disappearing. What happens is that they are decomposed by the action of fungi and microorganisms.

Gardeners will know how useful this decomposition process is in adding nutrients to the soil – many accelerate this breaking-down process by making compost and applying it to the roots of their plants which can then take advantage of the extra food.

Two different species of fungi growing side-by-side

Inocybe (left) and Russula (right). These two mushrooms although very close two each other are from different fungal genera. Neither of these fungi are likely to be edible but were found in the same area as Agaricus sp. and Deathcap (Amanita phalloides).
Photo courtesy: Sapphire McMullan-Fisher.

The dangers of picking mushrooms are increased as many people don’t realise that two mushrooms can grow close together but may be two different species of fungi altogether, and one or both may be poisonous.

Why are they here?

Deathcap mushrooms have been popping up more this year because the wet conditions favour their fruiting. Typically, they are more often seen with the early Autumn rains. These mushrooms are not turning up with any malicious intent, it’s just that the weather conditions are suitable.

Most fungi go unseen most of the time because they live within soil, wood or other substrates. We tend to notice them when they produce fruiting bodies. Like the fruit of plants that spread the seeds; mushrooms and their fruiting bodies spread the spores of the fungus. Although we don’t see most fungi most of the time, they perform important roles in our environment.

The Deathcap mushrooms are part of an important group of fungi in our ecosystems called mycorrhiza. Without mycorrhiza, most land-based plants would grow poorly or not at all in some cases. Deathcap mushrooms are often found under exotic trees like oaks, common in Canberra’s Parks and Gardens. The Deathcap is a mycorrhizal partner with these trees. This mushroom is a hitchhiker that came across with these imported plants.

What are they doing?

As a mycorrhizal fungus, the mushroom is carrying out an important job of getting micronutrients and water to its plant partner. Plants that have good mycrorrhizal partners have better nutrition, access to water and do better during drought. These mycorrhizal fungi live on the roots of their plants, and so often protect them from soil pathogens.

So the next time you see mushrooms and other fungi, you might stop to appreciate that they are working to help keep your local ecosystem healthy.

Get involved with Fungi

Are you passionate about Fungi and and want to learn more? Consider attending the three day Tasmanian Fungi Festival in Hobart, 26-29 April 2012, presented by Fungimap and NRM South.

Tasmanian Fungi Festival details:

Or why not join your local Fungi study group affiliated with Fungimap »

The Atlas of Living Australia is in partnership with Fungimap to develop a new FieldData tool for capturing details of Fungi found in the field and working on improving the information gathered about Fungimap’s target species. More on this later …

Dr John La Salle, Director of the Atlas of Living Australia

Dr John La Salle, Director of the Atlas of Living Australia

Dr John La Salle will take on the role as the Atlas’ Director for the next 18 months. John has been involved in the Atlas from its inception and played a key role in its establishment. As the Director of the Atlas, one of his main roles is working towards a secure future for the project by building a case for renewed government funding, maintaining partner engagement and searching for new opportunities.

John would like to thank the founding Director of the Atlas, Donald Hobern, for his invaluable contribution to the Atlas. Donald has left the Atlas to lead the Global Biodiversity Information Facility in Copenhagen – the biggest biodiversity informatics initiative in the world.

For more information contact lynne.sealie@csiro.au.

This tool allows you to search for a species available via the Atlas  (including at higher taxonomic levels) and map their distribution. The selection of taxa (species, genus etc) uses a method called auto-complete. As you enter letters, the system searches for taxa that match what you have typed. The auto-complete function should support browsers on any system including tablets.

Add to map options

Add to Map options

From the menu option, select “Add To Map” and then “Species”.

Species options

Species options

There are five add species options, choose which option suits your requirements:

Press “Next”.

The Upload points has an additional step to upload a user’s file. Follow the links for more information. Otherwise you will be presented with a screen like the below:

Species apply to area

Select an area for restricting the species occurrences mapped

If you have a predefined area already mapped, then an option is available to apply it: For example, “My Area”.

If you have already zoomed the map into a specific area of interest, then the ‘Current Extent’ option is available to show both specific species or all species in that zoomed area.

In the add “All species” option, “Australia” and the “World” are not available as defaults due to potential size problems.

Note the “Define new area” will involve an extra step (please refer to Add Area for additional information).

Press “Next” once the area has been defined and a new layer will be added to the list of layers on the left hand side of the screen and to the map, showing the species (or higher taxa) distribution.

Occurences in Current Extent

Occurences in Current Extent

NOTE: that the layer name can be edited in the legend as needed (see below).

Interact with the legend for the layer

Interact with the legend for the layer

The legend can be used to change the displayed view of  the species points. You can change the colour (now called Facet), opacity and size for the points manually.

If there are a large number of facet classes, a search box will be automatically generated above the facet list in the legend. You can use this search to filter/highlight any one or more classes that interest you. Once the classes have been selected, you can generate a new points layer that only contains those filtered/highlighted classes.

For detailed information on grouping by species attributes – faceting and filtering »

Search for a species by scientific or common name

To search for a species to add to the map, select the “Search for species by scientific or common name” radio button (this is the default).

Hint: “Species” in the Spatial Portal can be generalised to any higher taxonomic level e.g. genus, family, order or class.

Autoselection of names is available

Autoselection of names is available

Start typing the scientific or common name and a series of matching names are revealed in a drop down list. Select your required name.
If the name is not found, it may be because:

  • It may not be available yet in the Atlas.
  • It may be listed under a more recent scientific name or common name.
  • The spelling may have to be checked.

Once a name has been selected, press “Next”.

All known occurrences matching that name will be plotted on the map for your defined area.

The layer is added to the active layers list. This allows you to manage the various layers.

Points or Density Grids

There are two main ways to view species records – density grid and points. The user can toggle between the two views using the “Display as” radio button.  Currently the density grid is the default view for in excess of 2,000,000 occurrence records.

Density Grid_640

Density Grid View

Display as Points_640

Display as Points View

Species Occurrence Information pop-up

Clicking on the species point on the map (or on the density grid) will pop-up information about that occurrence and link to any related data.

Occurence details pop-up

If there are multiple observations for a location, you can page through the list, one occurrence record at a time by clicking on the arrow.

Species Layer Functions

After adding a species layer, a number of options are available in the left hand pane. The following annotated screenshots explain what they are.

Layer Options annotated

Layer Options annotated

Spatial Uncertainty

In the points view, the spatial uncertainty of each occurrence record may be displayed as a circle centred around each point. It uses the value of each point’s location spatial uncertainty (coordinate precision) in metres. By selecting the checkbox “Display spatial uncertainty as a circle” different coloured circles and radii lengths surround each occurrence point. Note that there are many records in the Atlas that do not have a value for spatial uncertainty.

The Uncertainty Legend:

  • Uncertainty known and less than 30 km, a white circle is used with the actual radius of uncertainty. (Zooming right into the occurrence point may be necessary to detect the white surrounding circle).
  • Uncertainty known and greater than 30 km, a green 30 km radius circle is used.
  • Uncertainty unknown, a yellow 30 km radius circle is used.
Spatial uncertainty displayed as circles

Spatial uncertainty displayed as circles

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 public but as a List owner, they can also be 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 not required further.

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.  If they are temporary, please remove them once the project or exercise has been completed.

A List can be used anywhere a single species can be used. The options are

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.

A species List can be created on the fly by pasting in any combination of scientific or common names or LSIDs (Life Science Identifiers) into the species selection multi-line text box and pressing the ‘Add’ button.

The names or IDs will be looked in the National Species List and a message will be displayed for those not found. 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.

 Create a Species List

Create list

Press the ‘click to search’ in the family column for ‘not found’ species to copy the species into the ‘Add from search’ text field. This uses a different search system using ‘auto-complete’ so you may try removing a few letters to allow the search for close names.

Species Assemblage No Match Species

Species Assemblage cannot match these species

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 ‘Tiger Moth’ in the figure above, will be added to the records list as ‘not found’.

Click to search in the records list, to copy the ‘not found’ common name into the species drop down list.

Once the List has been created, it will be saved and made public until you delete it.

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. The list of Lists is displayed and one or more Lists can be selected for use. 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.

Use Existing Species List

Limit to Area

‘Apply to an area’ limits the mapping of occurrence records to a predefined or a ‘defined on the fly’ area. See the image above. Defining a new area adds an area layer using any one of 14 options.

Click the ‘Next’ button.

Any predefined area (My Area) listed as a map layer in the top left layers list can be used for limiting the area used for mapping the species assemblage.

Species apply to area

The figures below are examples of mapping multiple species by the use of Lists-

Species Assemblage Points

Example of an Add to Map species assemblage

Species Assemblage Points Faceted by Scientific Name

Example of an Add to Map species assemblage faceted by scientific name

For more information on faceting and filtering »

Species Assemblage Density Grid

Example of an Add to Map species assemblage displayed as a Density grid

Click on the Display as ‘Density grid’ to change the map to display the species assemblage 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.

Species Assemblage Layer Metadata

Example of the metadata created for a species assemblage

Demonstration Youtube Video

By Lee Belbin, Geospatial Team Leader