This option will take any mapped point layer in the Spatial Portal and export it to the Biodiversity and Climate Change Virtual Laboratory site (bccvl). You would use this option only after cleaning/filtering your data to ensure that all records are fit for purpose for the analyses planned within bccvl. For example, you would want to remove duplicate records, records with poor spatial and temporal resolution or possibly records that have user assertions (user annotations) for say an SDM.
The primary way of cleaning records is to use the legend of the point layer, and select that facet (indexed variable) from the dropdown box to the right of “User defined colour”. You may want to examine some of the original Darwin Core terms such as “collectedBy” or “year”. You will certainly want to examine all of the “Record issues” and other facets in the class “Assertions”. The ALA and bccvl run joint workshops on the issues around filtering data in the ALA’s Spatial Portal and analysing it in the bccvl. To learn more, email firstname.lastname@example.org.
After clicking on “Export to bccvl”, you will get a window that will ask you to either login in to bccvl or to create a new account.
After you login, you will then be asked to authorize the ALA to access your bccvl account so that the point layer can be exported there…You can authorize or deny. If you deny, then the only way to get filtered ALA data to the bccvl is to export it from the Spatial Portal as a CSV file and then import it after loggin into bccvl. “Authorize” makes the process simple.
After you authorize access of the Spatial Portal to bccvl, the Spatial Portal will display a window detailing all of the mapped point layers.
The layer to export to bccvl will usually be the last (top) point layer as the older versions will usually represent partially filtered versions of that final layer.
Select the point layer or layers that you want to export to bccvl for analyses and press the “Next” button as shown below.
If the process goes to plan, you should see a new window that shows that the export has been successful. This window contains a link to bccvl. If you click on it, you will be taken directly to your data pages in bccvl and the layer name should be first on the list.
Greater impact through environmental infrastructure symposium
In May 2017, National Collaborative Research Infrastructure Strategy (NCRIS) facilities are coming together to host a Symposium to celebrate the achievements enabled by investment in research infrastructure.
More information will be coming in the New Year, but for now lock these dates into your calendar so that you can come and share these achievements with us.
What: Greater impact through environmental infrastructure symposium
When: 16-18th May 2017
The ALA is made possible by contributions from its many partners. It receives support from the Australian Government through the National Collaborative Research Infrastructure Strategy (NCRIS) and is hosted by CSIRO.
Dear Atlas of Living Australia friends,
As 2016 draws to a close, I’d like to take this opportunity to thank you for your ongoing support to the Atlas of Living Australia (ALA). It is you, as members of our community that have made our achievements possible and make us what we are today.
The end of the year is a time for reflection, and for the ALA 2016 has been very productive. Here are just a few highlights I’d like to share before we all head off on a well-deserved break over the holiday season.
Field data collection now better than ever
This year we proudly launched the first production release of BioCollect, our new data collection tool (replacing the old FieldData system), for collecting observation, survey and activity data. BioCollect is integrated with other ALA tools and allows you to easily create and manage projects and data collection surveys which provide a more seamless flow of biodiversity occurrence data into the ALA.
BioCollect supports the growing needs of both scientists wanting to engage the public in their research and the public wanting to participate in important scientific work. We are continuing to enhance and evolve the system in collaboration with our ever-growing community of users.
Continuing our global reach
Working with the Global Biodiversity Information Facility (GBIF), we continue to facilitate other countries to develop biodiversity information platforms using ALA e-infrastructure. The ALA’s open source platform is becoming a critical component within the GBIF network. Spain, France, Portugal, Costa Rica, Argentina, Brazil and Scotland have used ALA’s open infrastructure to help establish national biodiversity information portals, with several other countries investigating its use.
Indigenous Ecological Knowledge
In partnership with Indigenous communities working on country, we’re exploring the role of information management platforms in bridging the boundaries between traditional Indigenous ecological knowledge and western science, as well as empowering two-way participation in the sharing of biodiversity knowledge. This year we have made good progress to improve the relevance of the ALA website and software looking towards how using both knowledge systems can give a broader perspective on Australia’s amazing biodiversity.
For the first time, the 2016 ALA Science Symposium was held interstate and hosted by one of our partners, the Department of Parks and Wildlife in Perth, Western Australia. We had a full program, with many stimulating talks. Thank you to everyone who helped make the 2016 ALA Science Symposium such a success. This includes presenters, moderators, ALA staff, and also all the participants who contributed through attending and creating such a lively atmosphere.
The 2016 Science Symposium was such a success that next year we’re committed to making it even better. To make this happen, we’re joining forces with several other National Collaborative Research Infrastructure Strategy (NCRIS) facilities to co-host a combined Environmental Symposium. Keep an eye out for details in the early New Year.
A milestone achievement
In September we reached a pretty impressive milestone, with over eight billion records downloaded from the ALA. We’re pleased to see that so many people are getting value from the ALA and it goes to the heart of our open access principle – collect data once, make it freely accessible and discoverable, and use it many times!
New features and improvements
This year saw the launch of many new features and improvements to the ALA. The redesign of species profiles and improvements to search functionality, additional features to better share data across other platforms, and new functionality to improve how users download data just to name a few. We also upgraded the names management infrastructure to allow much faster updates to taxonomy and implemented an important feature to allow record owners to verify and comment on annotated records. We’re always working on improving the ALA site and will continue to make improvements in the New Year. If you have any suggestions for future improvements we’re always open to feedback.
Streamlining data cleaning and modelling
Throughout 2016 we teamed up with the Biodiversity and Climate Change Virtual Laboratory (BCCVL) to run a series of workshops on how to get the most out of the ALA’s Spatial Portal and BCCVL’s modelling tools. The workshops were run at conferences and events around the country from Perth to Hobart and many stops in between. We also worked together to better integrate the two platforms so that users are able to find, investigate and clean ALA occurrence records using the tools in the ALA and then, at the click of a button, push this data set directly to the BCCVL ready to be used in models.
In the classroom
The ALA is a wonderful resource for the classroom, and in 2016 we were successful in gaining accreditation through the Teacher Quality Institute (TQI) to run workshops for primary and secondary school teachers in the ACT. We ran our first accredited teacher workshop in November with 17 participants. Teacher workshops were also run through the Australian Association for Environmental Education and the Science Teachers’ Association of Victoria. Keep an eye open for more teacher workshops early in 2017.
The National Research Infrastructure Roadmap is out
You may have seen that Department of Education and Training has released the Draft 2016 National Research Infrastructure Roadmap which is available on the Department’s web page. The 2016 National Research Infrastructure Roadmap will be used to support future investment decisions that will ensure Australian researchers can access world class major national research infrastructure. The ALA looks forward to the outcomes of this.
Again, I would like to thank all of our colleagues, partners, collaborators and contributors who have made these achievements possible. I would also like to give a special thanks to all ALA staff. The many achievements listed above are a direct result of our hard-working ALA family.
Finally, I wish you a safe and happy break over the holiday season, and I look forward to an even bigger 2017.
John La Salle
Director Atlas of Living Australia
The Biodiversity and Climate Change Virtual Laboratory (BCCVL) is a ‘one stop modelling shop’ that simplifies the process of biodiversity-climate change modelling. The ALA is a collaborative open infrastructure that pulls together biodiversity data from multiple sources. This week we have released a collaborative project to streamline processes for people using ALA data and BCCVL modelling tools.
There are currently more than 60 million occurrence records in the ALA, based on specimens, field observations and surveys. Through the Spatial Portal the ALA also provides powerful mapping and analysis tools, allowing users to explore the information in new ways. For example, users can pull in species occurrence records and clean these based on a number of different factors, such as location uncertainty. Once cleaned, users can also conduct some preliminary data investigation such as histograms and scatter plots to better understand their data before using it in models.
BCCVL connects the biodiversity and climate change research community to Australia’s national computation infrastructure by integrating a suite of tools in a coherent online environment. The goal of the BCCVL is to integrate these tools and data sets with high-performance computers and major data storage facilities.
Currently the BCCVL offers its users live access to the raw ALA occurrence records. However, to clean this data users would have to download it, manually clean it, and then re-upload it into the BCCVL. At the end of our collaborative project, users will be able to find, investigate and clean ALA occurrence records using the tools in the ALA and then, at the click of a button, push this data set directly to the BCCVL ready to be used in models. Data can also come in the other way (i.e. from BCCVL) and then cleaned, refined or augmented in the ALA and returned to BCCVL. This integration promotes good data practices and will encourage more robust model outputs. It also allows the two NCRIS facilities to focus on their core strengths: BCCVL on modelling, and ALA on data aggregation, exploration and visualisation.
The collaboration between BCCVL and ALA is ongoing. The BCCVL is supported by the National eResearch Tools and Resources Project (NeCTAR), an initiative of the Australian Government being conducted as part of the Super Science Initiative and financed from the Education Investment Fund, Department of Industry, Innovation, Science, Research and Tertiary Education. The University of Melbourne is the lead agent for the delivery of the NeCTAR project and Griffith University is the sub-contractor. The ALA is funded by the Australian Government National Collaborative Infrastructure Strategy (NCRIS) and hosted by CSIRO.
For more information on BCCVL-ALA collaboration, visit ‘Fit for purpose’ data with the ALA.
One of our most prolific contributors to the ALA is Reiner Richter, a wildlife photographer from Victoria. He has been taking nature photographs as a hobby for many years and has submitted over 13,000 fantastic sightings to the ALA.
Reiner uses the ALA to assist with identification for species that he is less familiar with.
“If I know what the genus might be I will search for species within that genera that are nearby using the mapping tools,” Reiner said.
He also uses the ALA to find gaps in data then embarks on expeditions to fill them. A couple of years ago, he noticed a gap between Lakes Entrance and Orbost and upon searching there, he found a population of Austrocnemis splendida, a small damselfly that is quite rare in the state.
While searching for and photographing species, Reiner has made some interesting discoveries. His rediscovery of a Micraspis flavovittata, a ladybeetle thought to be extinct, garnered some attention in the mainstream media. From the unique markings, he knew on sight that this was a new species for him personally. Not finding an image of such a species anywhere on the web, he passed it on to experts, starting with Museum Victoria. He is hopeful that this species can get listed as critically endangered as a result.
One of the things Reiner finds most rewarding is to photograph fungi in winter.
“Many strange fungi remain unidentified as the kingdom is vast and there are few experts in the field, so relatively few species have been described,” Reiner said.
Please contact us if you would like to share how you use the ALA.
The scatterplot function links the sampled values of any two environmental variables on a species (or genus etc) with the map. Points on the scatterplot represent the environment found at each occurrence record, as given by the environmental variables of the two axes of the scatterplot.
The scatterplot (environmental space) and the map (geographic space) are linked. Dragging a rectangle over an area of the scatterplot to enclose occurrence points will highlight the corresponding points on the map. You can also define an active area on the map and have all occurrences within that area highlighted on the scatterplot.
From the menu option, select ‘Tools’ and then ‘Scatterplot’.
The scatterplot requires a minimum of three parameters – a species or taxonomic group and two environmental variables.
Any legend permits modification of the display of the associated layer. In the scatterplot tool, this means that both the points (occurrences) in both the map (geographic) and environmental (scatterplot) space. To activate the legend in the scatterplot, click on the ‘Species display setting’ button. This will create a floating legend that will permit rendering the points in both spaces on the basis of selected legend properties. For example, in the image at the top of the page, under the facet dropdown box on the legend, “Institution” was selected and the Apply button pressed. After a little while (for many points) the points on the scatterplot and the map will be coloured according to the institution facet.
For more detailed information on Scatterplot faceting »
A case study on using the scatterplot tool to investigate the distribution of Banksia integrifolia in Australia, is given by Dr Ben Raymond of the Australian Antarctic Division, Hobart.
Read the Case Study »
For Step 4, we are now using the general window for any type of environmental/contextual layer selection. If you tick the box next to “Display possible environments“, the scatterplot will be shaded (from dark meaning a small area of that environmental combination – to light meaning a large area of that environmental combination) to display what environmental combinations are possible – and not all are, thankfully.
In the context of the scatterplot, it is likely that you will want to use the ‘Add from search‘ box and either enter part of the name of the layer or its short name (e.g., Bio01 for “Temperature – annual mean”) and then check the box on the left of the name to select it. Ditto with the second layer. At the bottom of the window, you will see the number of layers selected and this should equal 2 before clicking on the next key (bottom right).
An alternative is to import the names of the two layers from a file – and this can be done from the top dropdown box. The names of the two selected layers can of course also be exported using the ‘Export set’ button at the bottom of the table. You can then re-import the list using the import option from the top dropdown box.
Once you have entered the name of the primary taxa (Eucalyptus camaldulensis), the (primary) occurrences are mapped.
The background taxa group is the genus Eucalyptus. This gives us a good indication of what environments the genus covers and what portion of that environment is covered by E. camaldulensis. These occurrences are only mapped on the scatterplot in orange in the background. The E. camaldulensis is shown by blue points. If the highlight records in the active area was selected, then those records would be ringed with a red circle.
In the worked example, we will use temperature (Temperature – annual mean (Bio01)) and precipitation (Precipitation – annual (Bio12)) as the two environmental variables to define the environment. Once these two variables have been added, the scatterplot is generated. As there is a large number of occurrences (Eucalyptus has over 240,000 records), processing can take up to a minute or so. The distribution of Eucalyptus (orange dots) covers a significant portion of the scatterplot, thereby indicating that the genus can handle a wide range of temperature and rainfall conditions. The majority of the distribution is below 2,500mm rainfall, with two higher rainfall extensions at low and high temperature. To learn more about the environment used by the genus, make it the primary taxa.
Eucalyptus camaldulensis is located toward the bottom of the scatterplot distribution and clearly follows the outline of the genus ‘envelope’ on the low precipitation end, but over a broad range of temperature. This suggests that E. camaldulensis is stereotypic of low rainfall adapted eucalyptus. However, it covers mean annual temperatures from 12°C to nearly 30°C – a very impressive range!
Let’s look at some of the outliers to see where they occur. First, the low temperature end. Drag a rectangle over the lower end occurrences on the scatterplot. This highlights the corresponding points on the map, near Cressy in Tasmania and Macedon in Victoria. The former is low altitude, but further south than the higher altitude Macedon.
Let’s do the same at the high temperature end to see where these occurrences are located. Drag the rectangle on the scatterplot and then examine the highlighted occurrences on the map. Not unexpectedly – the high temperature occurrences are found in the extreme north of Australia.
Note that the range of temperature and rainfall values of the rectangle are listed above the scatterplot. In this case, a mean annual temperature range of 25.6130°C to 28.0974°C and rainfall between 285.996mm and 485.908mm. Also note that there are 20 records selected
The selected occurrences could be used to create two new mapped layers – an ‘IN-group’ containing only those 20 occurrences and an ‘OUT-group’ containing all the rest. This option can be useful for filtering/separating out a subset of occurrences for further analysis in say the spatial prediction model. Also note that there are 73 occurrences that have one or two missing environmental values of temperature or rainfall. If an IN/OUT groups are created these occurrences are added to the OUT-group by default. If you click the checkbox saying ‘Select records with missing values’, then the corresponding occurrences will be highlighted on the map and added to the IN-group. In all cases, these occurrences are located off the terrestrial temperature and rainfall surfaces; they occur in the ocean. This may be due to the resolution of the surfaces or of the coastline or just inaccurate occurrence locations.
Next, let’s consider why E. camaldulensis doesn’t occur in a few environments on the scatterplot.
There is a hole in the distribution of E. camaldulensis at around 25°C and 600mm that is filled by other eucalypt species (shown by the orange Eucalyptus background points) so that environment exists in nature. But why are there no occurrences here? There are at least four possibilities:
The same situation doesn’t occur with the ‘dent’ in the environment at around 14°C and 2500mm. Obviously that environment doesn’t exist in Australia (at least not represented by the environmental layers we have chosen) – and it is therefore not surprising that no eucalypts are to be found. The eucalyptus background covers much of the potential environmental range indicating the ubiquity of the genus. The grey-scale of the ‘display possible environments in area’ indicate the size of the corresponding mapped areas, with black representing only a small area with this environment in Australia, and reversely white, a large area. For example, there are only small areas of Australia with extreme rainfall (around Tully in Northern Queensland), and a large area of very low rainfall. This can be examined further by examining the environmental layers: Temperature – annual mean (Bio01) and Precipitation – annual (Bio12).
Mean annual temperature and annual rainfall were chosen because these variables were very likely to constrain the spatial distribution of eucalyptus. You may wish to use the Prediction Tool (MaxEnt) to find out which environmental variables best seem to control the distribution of Eucalyptus camaldulensis.
By Lee Belbin, Geospatial Team Leader
This post has been written and produced by Emilie Ens from Macquarie University, Sydney.
Over the last couple of years the ALA has been working with the Yugul Mangi Rangers and Macquarie University ecologists to build cross-cultural biodiversity knowledge of SE Arnhem Land. Additionally the collaboration has helped develop Indigenous content in the ALA website and raise awareness nationally, about Indigenous science and biodiversity management. The team has just published a paper called “Putting Indigenous Conservation Policy into practice delivers biodiversity and cultural benefits“.
In July 2016, the team held a regional woman’s biodiversity and cultural knowledge sharing workshop at Ngilipitji in eastern Arnhem Land. Thirty five women attended from the three ranger groups in the region (Yugul Mangi Rangers from Ngukurr, Yirralka Rangers from Yirrkala and Numbirindi Rangers from Numbulwar) as well as the Ngukurr Yangbala (Young) Rangers. Ngilipitji was chosen as a mid-way point for the groups and because it lies close to the border of the Laynhapuy Indigenous Protected Area (managed by the Yirralka Rangers) and the proposed SE Arnhem Land Indigenous Protected Area (managed by the Yugul Mangi and Numbirindi Rangers under the Northern Land Council) and is considered a “shared management” zone.
The team conducted biodiversity surveys over three days and nights in an area that according to ALA data, had not been surveyed in the past. We set up 70 Elliot, 15 Cage, 6 Pitfall, 15 Funnel and 12 camera traps over three sites (Rocky hill, Bottom spring, Top spring) to detect mammals and reptiles. We conducted one night search around the outstation for geckoes, did plenty of fishing and made opportunistic sightings of species. Despite the remoteness of this Country, surprisingly we only found 4 skinks (Carlia munda, Cryptoblepharus metallicus), 5 geckoes (Gehyra australis, Heteronotia binoei), 2 water rats (Hydromys chrysogaster), 2 dingoes (Canis lupus dingo), 3 crows (Corvus orru), 8 Black Bream (Hephaestus fluiginosus) and freshwater crocodile’s (Crocodylus johnsoni) eyes shining at night in the creek. One feral cat, 2 cane toads and evidence of feral buffalo and pig were also seen. We found no frogs, small mammals, large reptiles or turtles. The lack of animal sightings was suggested as due to the weather being cold and at times windy and raining. However the presence of feral animals and possibility of past damaging late dry season wild fires were also discussed as possible causes.
At each site we did plant collections, pressed specimens and are still processing and identifying the species. However about 50 species were recorded, all were commonly known. Some lively knowledge exchange occurred around the plant species. The common medicinal plant Eucalyptus tetrodonta was called bambuja by the SE Arnhem mob and gadayka by the NE Arnhem ladies. All grasses were called wiji in Marra, mulmu in Yolngu matha and notho in Ngandi languages. The large Acacias (Acacia auriculiformis and A. aulacocarpa) were described as dukul in Ngandi, Ritharrngu and Ngalakan (SE Arnhem languages) and dhurrtji in Yolngu matha (NE Arnhem). Despite being relatively close in proximity, there were clear differences in language words for plants between SE and NE Arnhem Land.
In addition to exchange of language names and uses knowledge, senior Ngandi woman Cherry Wulumirr Daniels also facilitated cultural leadership and kinship discussions throughout the camp with her usual passion and command of everyone’s attention. On the last night, the Yirralka Rangers shared with everyone a cultural song and dance (manikay) about Ngilipitji that was recorded by their family members. They also taught the group a range of other songs and dances that often had environmental themes. This was followed by cultural performances and lessons from the Numbirindi Rangers and Ngukurr mob.
After the camp the Yirralka Rangers came to Ngukurr, many for the first time, and participated in an ALA workshop led by Rebecca Pirzl with input from Julie Roy, Yugul Mangi senior woman ranger. We downloaded the camera trap photos and shared all photos and videos with each other.
All the ladies had a fantastic time learning from each other and experiencing Country that many had never been to before. Although we only found a few animal species and common plant species, they were all significant records due to the lack of surveys in this area in the past. The knowledge exchange was deemed a success with annual exchanges and the need for more cross-cultural biodiversity surveys discussed.
Banbai nation people at Wattleridge Indigenous Protected Area in northern New South Wales are working with Michelle McKemey at the University of New England to develop season and fire calendars.
The calendars represent annual seasonal changes as well as biocultural factors that indicate the right, and wrong, time to burn. They are developed using results of ecological experiments, literature reviews, observations and cultural knowledge gathered through interviews. For more information read WINBA = FIRE, the Wattleridge IPA Fire and Seasons Calendar. The development of the WINBA = FIRE, Wattleridge Fire and Seasons calendar has been supported by the Firesticks Project.
The ALA is working with Michelle and her Indigenous collaborators to test an ALA prototype for an online interactive Indigenous seasonal calendar. This online platform will visualise and reflect the Indigenous knowledge contained within seasonal calendars and the context for which they were developed. The project will also create some opportunities for two-way sharing by linking to other biodiversity information contained in the ALA.
This work is part ALA’s Indigenous Ecological Knowledge plan which is exploring the role of various information management platforms in bridging the boundaries between traditional Indigenous knowledge and western science.