Health – https://archive.gaiaresources.com.au Environmental Technology Consultants Thu, 29 Feb 2024 03:47:38 +0000 en-AU hourly 1 https://wordpress.org/?v=4.9.1 Our mobile apps – a recap https://archive.gaiaresources.com.au/mobile-apps-recap/ Thu, 18 Mar 2021 00:30:26 +0000 https://archive.gaiaresources.com.au/?p=9051 Following on from our recent posts on the NAFI Fire Information and Slug Sleuth apps, we thought it would be good to highlight more of our work in mobile app development. Over the years we have developed quite a range of apps in the biodiversity, fire, parks and citizen science sectors. In the citizen science... Continue reading →

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Following on from our recent posts on the NAFI Fire Information and Slug Sleuth apps, we thought it would be good to highlight more of our work in mobile app development.

Over the years we have developed quite a range of apps in the biodiversity, fire, parks and citizen science sectors.

A range of mobile apps currently available in the App Stores

In the citizen science sector, a number of our apps have helped scientists engage with citizenry to monitor and report sightings of species of interest in order to broaden their research input. Our most long-running partnership is with the River Guardians team in WA’s Department of Biodiversity, Conservation and Attractions, where the Dolphin Watch app has enabled the monitoring of the small population of Indo-pacific bottle-nosed dolphins (Tursiops aduncus) in Perth’s Swan and Canning River estuary. Over nearly a decade we have put enormous effort into supporting this significant program, where up to 1000 trained local citizens have contributed images, observations and surveys to the project. The project has since been extended to other sites in WA, such as Broome and Mandurah.

Two more recent project to aid species conservation were the I Spy Koala app, developed in 2019 for the NSW Department of Planning, Industry and Environment (DPIE) for the collection of koala observation and survey data to improve the flow of Koala observation data into NSW planning and decisions tools; and Slug Sleuth, , an app that aims to help scientists, locals and visitors to collect observation data for slugs and snails within Mount Kaputar National Park and adjacent Nandewar Ranges within NSW, but especially the threatened Mt Kaputar giant pink slug (Triboniophorus< aff. graeffei).

Significantly, both these apps were developed to submit data to the NPWS BioSys repository. BioSys is an open-source, standards-based data management system built specifically for biological data. The system has a flexible data schema model that allows users to create a schema specific to the structure of their data, and that can apply to just about any biological and ecological data.

The Urban Wildlife app was developed for the NESP Clean Air and Urban Landcapes Hub, based primarily at the University of Melbourne, and contained multiple projects in which to record sightings of bell frogs, beneficial insects, flying foxes, or possums and gliders, usually across all states and territories in Australia.

Another take on the utility of apps – if they can help observe and conserve biodiversity, can they also assist in managing its major threatening processes? Here’s a couple of examples that we’ve brought into production in the last couple of years.

A range of mobile apps currently available in the App Stores

The NAFI Fire Information app brings the most used fire information resource for land managers in northern Australia to a mobile device, providing a constant eye on local bushfire threats.

And, the Essential Service Volunteers app helps volunteers automatically track the duration, location and type of work they undertook, an ID card service to show they’re an approved member of a legitimate volunteer essential service, and access to community discounts for firies and others essential volunteers.

And for the Wildcare Helpline app we worked with the Department of Biodiversity, Conservation and Attractions (DBCA) to develop an app that provides a service for the WA public who find sick or injured native wildlife and are seeking advice on where to find care for the animal.

We’ve also developed a number of apps along with DBCA and Trails WA to help the community enjoy the natural beauty of WA as well!. Camping Mate and Marine Parks WA are both DBCA apps aimed at ensuring the user maximises their experience of the Park facilities in WA, both on land ad water. And Trails WA provides detailed information – even when off-grid – to hikers hitting the extensive bike and walking tracks in WA.

And finally, it’s worth noting we also develop apps that have a very restricted purpose. The Mosquito Monitoring App is the first for the Atlas of Environmental Health (AEH). It was made specifically for the use of Environmental Health Officers within WA local governments. More recently, the AEH and the Mosquito Monitoring app have become useful in the Victorian health arena.

You can read more about our work on mobile apps over the last decade, or check out our current mobile apps in the Apple and Android app stores. (Other apps we’ve developed can be found on our client app stores.)

If you’re interested in how our mobile data collection apps could help your organisation, feel free to email me, or start a chat with us via Facebook, Twitter or LinkedIn.

Alex

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Evidence-based planning for resilient World Heritage Areas https://archive.gaiaresources.com.au/planning-for-resilient-whas/ Wed, 23 Sep 2020 00:00:11 +0000 https://archive.gaiaresources.com.au/?p=8564 Yesterday I attended an online event discussing planning for resilient World Heritage Areas, focussing on case studies in the Gondwanan rainforests of NE NSW and SE Queensland. The event was part of the Climate Change, Fire, and Biodiversity webinar series, co-hosted by the NESP Threatened Species Recovery and Earth Systems and Climate Change Hubs. Twenty... Continue reading →

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Yesterday I attended an online event discussing planning for resilient World Heritage Areas, focussing on case studies in the Gondwanan rainforests of NE NSW and SE Queensland. The event was part of the Climate Change, Fire, and Biodiversity webinar series, co-hosted by the NESP Threatened Species Recovery and Earth Systems and Climate Change Hubs.

Twenty World Heritage Areas are recognised in Australia by UNESCO for their unique cultural, geographical, and biological diversity. While these areas support outstanding universal values, they are under risk from disease, invasive species, and declining ecosystem processes. The speakers and panellists, drawn from the scientific community and on-the-ground conservation practitioners, discussed the benefits and challenges of integrating climate change and biodiversity knowledge in developing adaptive management plans to build more resilience in both species and ecosystems. They also clearly identified that existing ecological pressures are being exacerbated by a rapidly changing climate.

There were two featured speakers and five panellists discussing these pressing conservation issues – you can read more about each of them here.

Melinda Laidlaw, a Senior Ecologist with the Queensland Herbarium, gave a fascinating talk on a number of the decision tools employed for modelling past, current and future species habitats and investigating the impacts of climate change on the Gondwana Rainforests of Australia World Heritage Area.

Density of terrestrial threatened flora habitat across Queensland pre-clearing

Density of terrestrial threatened flora habitat across Queensland pre-clearing

Density of terrestrial threatened flora habitat remaining as remnant vegetation in 2015.

Density of terrestrial threatened flora habitat remaining as remnant vegetation in 2015

Source: State of the Environment – Queensland Department of Environment and Science.


 
Dave Newell, a Senior Lecturer at Southern Cross University, spoke passionately about his work on understanding the ecology of endangered amphibians, most of which are narrow range endemics susceptible to climate change and disease impacts. Dave and his students’ work in the World Heritage rainforests of northern NSW over several decades has improved conservation outcomes for some of Australia’s most unique frogs.

Dave Newell - illustrating the process for modelling rainforest frog distributions

Dave Newell – illustrating in more detail the process for modelling potential rainforest frog distributions

In response to audience questions, the panellists also discussed other threatening processes like extreme bushfire events and invasive diseases such as Myrtle Rust, the importance of new research into understanding the importance of ‘cloud water’ as a key survival strategy for some montane species, and the necessity of on-the-ground community coordination of conservation efforts.

I will add a link to the full webinar recording when it becomes available, or you will find it here in coming days.

The next webinar in this series is ‘Carbon sequestration & biodiversity: valuing & managing carbon-rich systems‘, scheduled for Tue, 13 October 2020 – I commend this series to you.

Species habitat modelling is an area I’ve long been interested in (I was a fairly early user of BIOCLIM in my work at the Royal Botanic Gardens Sydney, too many years ago) and more recently wrote on the utility of using the Biodiversity and Climate Change Virtual Laboratory (BCCVL).

Gaia Resources has worked with another NESP Hub – Clean Air Urban Landscapes – in recent years to build their Urban Wildlife mobile app. If you’d like to know more about how Gaia Resources could work with you in this area, then please drop me a line at alex.chapman@gaiaresources.com.au, or connect with us on TwitterLinkedIn or Facebook.

Alex

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Dieback Conference 2020 https://archive.gaiaresources.com.au/dieback-conference-2020/ Thu, 17 Sep 2020 00:00:00 +0000 https://archive.gaiaresources.com.au/?p=8533 On Friday 11th September 2020 Piers and I attended the Dieback Information Group Conference and South Coast NRM Dieback Information Forum, where speakers presented a range of forward-thinking planning and management options for the control of Phytophthora Dieback disease and other pathogenic key threatening processes. The conference itself, organised by the Dieback Working Group and... Continue reading →

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On Friday 11th September 2020 Piers and I attended the Dieback Information Group Conference and South Coast NRM Dieback Information Forum, where speakers presented a range of forward-thinking planning and management options for the control of Phytophthora Dieback disease and other pathogenic key threatening processes. The conference itself, organised by the Dieback Working Group and the South Coast NRM, was very informative, with engaging discussions and a range of hands-on demonstrations.

This years theme was Phytophthora Dieback – Tools for the Future, covering a range of contemporary topics such as recent developments in research and technology, and insights on industry engagement and land management. As with many events during the COVID-19 situation, the conference allowed the opportunity for experts, speakers and attendees to join together in person or online to contribute from local, state and international perspectives.

Some significant highlights for us included:

  • the chance to catch up with many of our south coast clients
  • learning about their work current practices and future directions, and how Gaia Resources can help
  • the potential use of Phytophthora Dieback management practices in other industries, e.g. in managing other soil-borne diseases
  • seeing how management goals have shifted over the years in response to previous management outcomes

The best highlight for me was the field trip to the beautiful Wireless Hill Park for a demonstration of Phytophthora Dieback management practices.

Tilo Massenbauer or Tilomass Consulting discusses the dynamics of public behavioural change

A demonstration of sampling a Phytophthora Dieback infested plant specimen

Anigozanthos manglesii at Wireless Hill Park, Perth

Diuris corymbosa at Wireless Hill Park, Perth

If you’d like to know more about our work in this area, please drop me a line at tracey.cousens@gaiaresources.com.au, or connect with us on TwitterLinkedIn or Facebook.

Tracey

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Introducing Kiri the service dog (in training) https://archive.gaiaresources.com.au/introducing-kiri/ Wed, 24 Jul 2019 05:15:43 +0000 https://archive.gaiaresources.com.au/?p=7004 Imagine your typical office environment in a high-rise building: long hours spent indoors in front of computers, low interaction between people, high stress levels, no grass, and certain expectations on cleanliness. These environments are hardly the place for animals… or are they? Study after study has shown the immediate benefits of animals in the workplace.... Continue reading →

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Imagine your typical office environment in a high-rise building: long hours spent indoors in front of computers, low interaction between people, high stress levels, no grass, and certain expectations on cleanliness. These environments are hardly the place for animals… or are they?

Study after study has shown the immediate benefits of animals in the workplace. That’s where Gaia’s latest employee, Kiri the boxer puppy, comes in. Kiri is training to be a service dog, which requires exposing her to as many sights, smells and sounds as possible during the age of 8-12 weeks.

Introducing Kiri, the service dog in training.

Piers and the Flux team have very kindly allowed me to bring her into the Perth office a couple of days a week to facilitate this training, which in turn has had a very positive impact on not only the Gaia staff, but the many other workers that share the floors at Flux.

Some things I’ve noticed since bringing Kiri in to work:

  • I have gotten to know more people in two weeks than in the entire 18 months we’ve been at Flux, because they all come over for a chat and a cuddle.
  • People smile just looking at her. And they turn to mush when you let them have a pat or a cuddle.
  • In meetings, the overall vibe is a lot more relaxed when Kiri is present.
  • Productivity tends to increase on the days I bring Kiri in. Although she may be a (very cute) distraction, when staff return to their work they are in a better frame of mind.
Kiri and Piers

Productivity has been shown to increase when a dog is brought to the workplace. It is, however, occasionally compromised!

For me personally, I feel a bit distracted and overwhelmed at times because I am constantly being pulled from my work to tend to Kiri’s needs, but I know things will become significantly easier once she is out of the puppy phase, toilet trained, and less inclined to munch on computer cables.

And when she curls up in my arms, all stress melts away.

Kiri and staff

If you’d like to talk about the benefits of service dogs in the workplace (or just come in to meet Kiri!) then leave a comment below, start a chat with me via Facebook, Twitter or LinkedIn, or email me directly via tracey.cousens@gaiaresources.com.au.

Tracey

Resources

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NatureLink and the Circular Economy https://archive.gaiaresources.com.au/naturelink-circular-economy/ Wed, 17 Jul 2019 06:43:02 +0000 https://archive.gaiaresources.com.au/?p=6932 I had the good fortune to attend two very interesting events recently. And if I learnt anything from these two rather different focus groups it’s that there is a real momentum across business and the community to work smarter to address the serious environmental issues we are facing. The key reference binding these two events... Continue reading →

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I had the good fortune to attend two very interesting events recently. And if I learnt anything from these two rather different focus groups it’s that there is a real momentum across business and the community to work smarter to address the serious environmental issues we are facing.

The key reference binding these two events was the United Nations 17 Sustainable Development Goals at the core of the UN’s 2030 Agenda for Sustainable Development.

UN Sustainability Goals

The UN’s 17 Sustainable Development Goals

NatureLink Perth is a relatively new initiative hosted by Murdoch Unversity that aims to provide a hub for collaboration between diverse stakeholders to integrate nature into our city, sustain our world-class biodiversity, and provide a healthy, liveable city that benefits the economy, environment and its people.

The NatureLink Perth Symposium 2019 was held on the 4 July in the Kim Beazley Lecture Theatre at Murdoch University. The Symposium provided collaborative space to discuss efforts to enable nature-sensitive urban design and nurture a biodiverse, liveable city. It was attended by a diverse set of stakeholders, with some 202 registered participants including 83 organisations, and provided many opportunities for networking and input on the key goals and challenges.

Direct engagement and input from attendees using an interactive presentation platform was an excellent and efficient method for immediately capturing audience responses and feedback for later reference and sharing. Five key issues were presented and formed the basis of the panel discussions at the core of the day (each with a lead panelist).

Planning: How can State and Local Governments work together to better integrate biodiversity and green-space into planning at all levels? (Renata Zelinova, WALGA)
Fire Management: What are the conflicting elements of bushfire management and biodiversity conservation? How can we balance them to benefit both? (Tim McNaught, DFES)
Community Awareness: What facilities, education and community engagement programs should we target to better connect people with nature and sustain biodiversity? (Carmen Lawrence, CCWA/UWA)
Design Implementation: What are the challenges in getting approval for nature sensitive urban design and how can we improve design regulations to mainstream it? (Chris Green, UDIA)
Biodiversity Audit: What are the critical information gaps in biodiversity info and how can we obtain the information needed and collect it innovatively? (Richard Hobbs, UWA)
Five NatureLink focus areas

Five NatureLink focus areas

After the extended discussion session, where some quite passionate statements from both panellists and audience about clearing for development, loss of species, habitat and expertise, and the need to integrate and liberate knowledge, attendees were asked to indicate what they considered their top three priorities. The resulting graph, from 118 individuals, is shown below – improving planning and building regulation were considered key priorities, as was increased community awareness, engagement and advocacy.

Naturelink top three priorities

Naturelink panel discussion – top three priorities

In the afternoon session we heard from a number of the brilliant young NatureLink interns, most about to complete their studies, as well as local case studies on nature projects – Cockburn Community Wildlife Corridor (Sue Marsh), Saving Urban Turtles (Anthony Santoro, Murdoch U.), and Piney Lakes design trends (Kelly Fowler, City of Melville). The final keynote by Tom Hatton (EPA) was an inspiring call to listen to and work with the next generation, for the future. The take-home message to me was that local actions are the only real way to achieve global outcomes.

The immediate outcome of the symposium for the NatureLink team was to how to move into their collaborative phase using the information provided at the symposium. A precis of these considerations by this smaller workshop was distributed.

The following day I attended a morning session on The Circular Economy, organised by the Advanced Manufacturing Growth Centre (AMGC) and hosted by the WA Chamber of Commerce and Industry (CCIWA).

The ‘Circular Economy’ is a strategy for changing the way to produce, assemble, sell and use products to minimise waste and to reduce environmental impact, while being advantageous to business by maximising the use of valuable resources and contributing to innovation, growth and job creation.

The graphic at right simply illustrates the key difference between a linear and circular economy. The keynote speaker proposed that to the ‘4 Rs’ of Return, Reuse, Repair and Recycle can be added a fifth – Re-form.

Linear vs Circular_economy

Linear vs Circular economies

The keynote speaker was Professor Veena Sahajwalla, Director of the UNSW SMaRT Centre for Sustainable Materials Research and Technology. Veena and her team are working closely with industry partners to deliver the new science, processes and technologies that will drive the redirection of many of the world’s most challenging waste streams away from landfills and back into production; simultaneously reducing costs to alleviating pressures on the environment.

She is reimagining the global supply chain by demonstrating the viability of ‘mining’ our overburdened landfills to harness the wealth of useful elements like carbon, hydrogen and materials like silica, titania and metals embedded in our waste. One of the key elements to this vision is the implementation of smart micro-factories that can operate on a site as small as 50 square metres and can be located wherever waste may be stockpiled.

To round out this line of thought about “thinking global, acting local”, I happened to read an article the following day entitled Geoengineer the Planet? More Scientists Now Say It Must Be an Option. While it looked at a range of planetary-scale technologies for ameliorating global warming, it ended with a very local solution, which made me reflect on the way nature and human technology can co-exist in the future world. Here’s one quote from the article to finish.

In fact, natural regrowth is usually better than planting, since “allowing nature to choose which species predominate during natural regeneration allows for local adaptation and higher functional diversity,” says Robin Chazdon, an ecologist at the University of Connecticut. A study published in March by 87 researchers, including Chazdon, concluded that “secondary forests recover remarkably fast” with 80 percent of their species typically back in 20 years and 100 percent in 50 years.

It looks like it could be a win-win, delivering a climate payoff on the scale of geoengineering without any of the downsides. Tim Lenton of Exeter University, a proponent of research into geoengineering, says it could be an ideal solution. “I am against introducing new forcings such as sulphate aerosol injection in the stratosphere,” he says. “But I am in favor of emulating and enhancing natural feedback loops and cycles, such as regenerating degraded forests.”

It would, he says, strengthen the biosphere’s natural forces of self-regulation that British scientist James Lovelock has termed Gaia. Lenton has a new term for what is required. Not geoengineering, but Gaia-engineering.

If you’d like to talk about how our Gaia-software-engineering can help with your environmental projects or about any of the ideas presented here, then leave a comment below, start a chat with me via Facebook, Twitter or LinkedIn, or email me directly via alex.chapman@gaiaresources.com.au.

Alex

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Notify Now – Victoria launches its Animal Disease Notification App https://archive.gaiaresources.com.au/notify-now-victoria-launches-animal-disease-notification-app/ Wed, 19 Jun 2019 02:48:43 +0000 https://archive.gaiaresources.com.au/?p=6899 This week marks the launch by the Minister for Agriculture Jaclyn Symes of a new mobile application called “Notify Now” that Gaia Resources has developed for the Chief Veterinary Officer’s Unit in the Victorian Department of Jobs, Precincts and Regions (DJPR). This workflow-driven Animal Disease Notification app will be available on iOS and Android devices,... Continue reading →

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This week marks the launch by the Minister for Agriculture Jaclyn Symes of a new mobile application called “Notify Now” that Gaia Resources has developed for the Chief Veterinary Officer’s Unit in the Victorian Department of Jobs, Precincts and Regions (DJPR). This workflow-driven Animal Disease Notification app will be available on iOS and Android devices, and our team have worked really hard to design and build something that will streamline and capture all the information a vet, animal owner or property owner needs to supply when they spot a ‘notifiable’ animal health concern.

Once the Terms and Conditions are accepted, one can call an emergency hotline, find out more information about notifiable diseases, or start filling out a new notification. As the info link tells us “Early recognition of a serious or exotic animal disease is one of the most important factors influencing the chance of controlling the disease and reducing economic and social impact on the whole community.”

   
The Home page of the app (left) provides a number of resources to start a notification, find out more information or provide feedback. A graphic based pick list (right) allows for quick selection of an animal type before moving to the next step in the workflow.

Our client Sally Salmon at the Chief Veterinary Officer’s Unit, gives us the back story:

“Agriculture Victoria engaged Gaia Resources to develop a smart phone app that would allow users to easily and quickly notify the Department of the presence or suspicion of notifiable animal diseases. The app is primarily directed to vets, but it can also be used by animal owners, primary producers, livestock agents and other people who work with animals.”

“The key parts of the app are the ability to call the Exotic Animal Disease hotline, add geo-located pictures to the submission, and include all the details required under the Livestock Disease Control Act 1994.  The information goes directly to the Chief Veterinary Officer’s Unit email inbox.”

   
The map and geocoding feature (left) reduces time to enter address details; and the form entry details – which include pick lists and conditional field display (right) – are compiled along with photographs into an email notification. 

“The development included testing phases with a large number of Agriculture Victoria staff.

The app is available now on the App Store and Google Play, just search for ‘Notify Now’.”

“More information on notifiable diseases is available at the AgVic web site, http://agriculture.vic.gov.au/agriculture/pests-diseases-and-weeds/animal-diseases/notifiable-diseases.”

We are looking forward to seeing how vets and animal owners across Victoria think of the app and how much easier it makes reporting over the manual PDF form download approach. As with so many professions, it makes a big difference if you can apply some technological smarts to help people ‘find time’ and focus on their core work. This includes time saved by the staff at DJPR who can quickly act on a submitted notification.

As a side note, our team has increasingly been working on Health-related projects, and in this context – I would just like to draw attention to the interrelationships between human health, environmental health and animal health. It has been interesting to pick up through discussions and research that a “One Health” concept is seen as an important component of an effective and holistic health system; that we need to consider the health of our animals and food chain, as well as the health of the environment we live in.

In time we would like to help government agencies develop analytics capabilities by integrating these systems that might ‘live’ in different agencies or beyond their own servers, to share these different datasets and to monitor trends and relationships. Some of our clients are already reaching out to use technology to do this, and we looking forward to working with them to achieve their objectives.

Feel free to drop send me an email if you want to find out more, or start a conversation with us on social media via FacebookTwitter or LinkedIn.

Chris

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Data Standards in Environmental Health https://archive.gaiaresources.com.au/data-standards-environmental-health/ Wed, 20 Feb 2019 02:38:37 +0000 https://archive.gaiaresources.com.au/?p=6502 Back in December I wrote about some presentations that I did for the Indo-Pacific Centre for Health Security, and mentioned that one of the points that I raised to the attendees was about data standards. At Gaia Resources we’ve been heavily involved in data standards since the early days of the company (and before, in... Continue reading →

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Back in December I wrote about some presentations that I did for the Indo-Pacific Centre for Health Security, and mentioned that one of the points that I raised to the attendees was about data standards.

At Gaia Resources we’ve been heavily involved in data standards since the early days of the company (and before, in some cases!).  Personally, I have been involved in the reviews of standards like the TDWG Access Protocol for Information Retrieval (TAPIR), and have implemented toolkits to deliver data in the Darwin Core exchange standard.  In previous roles representing Museums I’ve also worked on standards approaches with the Faunal Collections Informatics Group, that supports the Council of the Heads of Australian Faunal Collections.

Alex has a similar background, except from the botanical side. He’s been involved in the technical groups around the Council of the Heads of Australasian Herbaria, specifically with the Herbarium Information Systems Committee that developed the national herbarium specimen data exchange standard HISPID, and was for six years the Oceania representative in the international working group Biodiversity Information Standards (TDWG).  Along the way, we’ve all seen and used a range of data standards, unique identifier approaches, metadata standards, exchange standards – and had a lot of hair pulling (we”, metaphorically in my case).

But, why do you need data standards? Let’s look at an example, using something we know pretty well.

In the states of Western Australia and Victoria, where we have implemented the Atlas of Environmental Health.  This has become a de facto data standard for this aspect of the Environmental Health domain.  The Atlas is made freely available to all Local Government Authorities to use in those states through the Departments of Health and Health and Human Services respectively, and this was the first time that a state-wide picture of mosquito trapping results could be implemented without significant data collation efforts.  With a few clicks, you can generate a current map of mosquito populations, like this one we have shown many times before for Victoria:

This map (in the system, not this one above) is dynamic, and so it is constantly up to date with the latest population information.  Right now, to do this for the whole country, you’d have to do the following:

  • know what you are looking for (e.g. the size of mosquito populations across Australia),
  • extract the data from each of the States from their own systems (some use Access databases, others commercial software, or the Atlas, or other tools),
  • undertake an exercise that would look across all of the datasets that have been provided, and work out which fields are the same (the ones containing the coordinates of the observations, species names, dates and abundance figures – which hopefully are all contained in all datasets),
  • migrate the data into a single data store, working through things like blanks, spelling mistakes, outdated taxonomy, different coordinate reference systems, etc, and
  • then pull this data into a spatial system of some sorts to draw the map shown above.

Frankly, by the time this is done manually – which could take weeks – the information will be so out of date it will be next to useless.  However, if the three data standards above were implemented the process would be:

  • all jurisdictions extract the data from their systems (which are compliant with the data standards) into the data exchange standard, which is provided with metadata in accordance to the standard,
  • the data is ingested into a new data store (and since all are compliant with the data exchange standard, this is much simpler), with some quality control implemented (still looking at the blanks, spelling mistakes, etc), and
  • the data is pulled out into a spatial system for mapping.

This second eventuality should take a matter of minutes to do, assuming that everyone is compliant with the standards.  When groups like the Indo-Pacific Centre for Health Security, or the National Arbovirus and Malaria Advisory Committee meet up they look at these sorts of reports for each State in paper or digital forms, so there’s a lot of different ways in which that data is presented (we’ve presented at NAMAC once before on the Atlas of Environmental Health).

So, how can we improve on this situation? I’m always fired up when solving interesting problems and as a result I’ve been sketching out ideas on various notebooks while I’ve been researching the area of data standards in the Environmental Health field since late last year, so here’s my take on a way forward.

Firstly, if we were starting from scratch here, what sort of data standards do we need?  At the very least, there should be three data standards developed for the Environmental Health area, namely:

  • Metadata standards – standards that we can use to describe the data itself (e.g. this data contains information about mosquito monitoring, ranges from this date to that date, covering the state of Western Australia, etc)
  • Data standards – the standard set of fields that we can use in describing the data itself (e.g. using unique identifiers, fields for genus, species, date trapped, time trapped, number of individuals, the weather conditions, controlled vocabularies,  etc), and
  • Data exchange standards – a set of fields that can be used in a data extract so that when this data is provided from one group to another it can be readily ingested and used (e.g. genus and species as a single field, date trapped, viruses present, etc).

It’s more than likely there would be many extensions to each, both in terms of digging deeper into controlled vocabularies and unique identifiers, or also in looking at the different aspects of environmental health (e.g. mosquito monitoring fields would be quite different from water quality ones).

I then thought through our work on the Mosquito Monitoring module of the Atlas of Environmental Health. The Atlas allows Environmental Health officers to go out into the environment, and monitor the populations and species diversity of mosquitoes, including capturing them in traps.  The mosquitoes can be then taken to a lab, identified to species level and they can also be tested to see if they carry diseases that will impact on people’s health. From this information, then the Environmental Health officer can determine the best course of action to take to control the mosquito populations in the environment.

At a very simplistic level, this simple workflow got me thinking of Environmental Health” as a combination of the two domains – “Environment” and “Health”.  In one of my whiteboard sessions, I ended up drawing a Venn diagram that got me thinking… there must be plenty of data standards within each of these areas that I could potentially point to and use.

Indeed, for both of these domains, there are a number of existing data standards that can potentially be used to bootstrap the development of new data standards.  As a rough first pass, here’s some of the potential standards from the disciplines of “Environment” and “Health” that could be of use… it’s by no means exhaustive, but there are a range of different ways to capitalise on this information.

Standard Environment Health
Metadata Standards Ecological Markup Language Metadata Online Registry
Data Standards Life Science Identifiers

International Union for the Conservation of Nature Conservation Status

Pathology and Laboratory Medicine Technical Framework 

International Classification of Diseases

Systematized Nomenclature of Medicine

Logical Observation Identifiers Names and Codes

Data Exchange Standards Darwin Core

Herbarium Information Standards and Protocols for the Interchange of Data (HISPID v.5)

Information Transfer Format 2

Access to Biological Collections Data

Health Level Seven

Statistical Data and Metadata eXchange

I’m sure there are other standards out there that I’ve missed, but it seems to me that there is still a fair bit of work still needed to put together a consolidated set of standards for the Environmental Health area, that matches the needs across the various parts of the field.

I wanted to also be clear that I’m not advocating that everyone needs to use the same system or product, which is often confused with using the same data standard.  The two should be separate so that there can be improvements, contention, and competition so that these systems and products improve. Otherwise, they will stagnate, especially under a monopoly arrangement when one product is prescribed for use.  The key is that all the different systems should use the same data standards, or support the use of the same data exchange standards to ensure data can flow between systems.

If the same data standard was under the hood of the various systems, authorities would be able to readily respond to incidents in a much faster turnaround time.  As a result, the world might just be a little bit better…

If you can think of other standards that we should consider (or you know of some that I just couldn’t find), then please drop me a line, or start a conversation on FacebookTwitter or LinkedIn.  I’d like to hear what you think, and how we can compile more resources on this!

Piers

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Mosquito ground surveillance – an update https://archive.gaiaresources.com.au/mosquito-ground-surveillance/ Tue, 15 Jan 2019 00:00:59 +0000 https://archive.gaiaresources.com.au/?p=6357 When Jake and I went across to Melbourne for the FOSS4G conference in November, I took the opportunity to catch up with some of our Victorian clients. One in particular was the Department of Health and Human Services (DHHS) whom we work closely with on the Atlas of Environmental Health and mosquito monitoring. It was great... Continue reading →

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When Jake and I went across to Melbourne for the FOSS4G conference in November, I took the opportunity to catch up with some of our Victorian clients. One in particular was the Department of Health and Human Services (DHHS) whom we work closely with on the Atlas of Environmental Health and mosquito monitoring. It was great to grab a coffee and catch up with a few of the staff there who I hadn’t met  before except across video conferencing and e-mails. Also it was a nice way to mix up and end a week otherwise spent listening to presentations about spatial systems and products.

There’s no substitute for face-to-face time when you want to learn about your client’s business and state of mind. By meeting with the public health entomologist, epidemiologists and analytics officers in the Communicable Disease Prevention and Control team I was able to learn a lot about business context and challenges around data, systems and reporting, and also the relationship between communicable diseases and on-ground mosquito monitoring activities. Fortnightly reporting and access to solid, accurate data is critical to fortnightly reporting and managing risk across a range of infections and diseases. Somehow the emails we are so used to using and phone calls boil down to just what you need to know for an immediate task or issue. The context can easily be lost, or not fully translated compared to when you are physically present and seeing what your clients are dealing with.

This trip didn’t have a field excursion like the one we did back in 2017 (see link to that blog here), but just as interesting I was able to sit down with an analytics officer and see how DHHS are tapping into the Atlas and other systems to build up their reporting outputs through PowerBI. Part of our latest phase of work with these guys to build an Application Programming Interface (API) so that analytics packages could draw data from the Atlas and combine that with other Health systems data (e.g. health facilities and their capacity to deal with outbreaks).

The fortnightly reports are part of critical presentations that senior officials in DHHS use to make strategic decisions for the health of Victorians and their facilities. Apart from keeping an eye out for Ross River Virus, health departments in Australia need to monitor for Murray Valley encephalitis virus,  Barmah Forest virus and dengue virus. Lately, Buruli – known as the Bairnsdale ulcer in Victoria, and the Daintree ulcer in Queensland –  has been making the news in Victoria (click here for the Victorian health alert). It is an infection caused by a flesh eating bacteria called Mycobacterium ulcerans that has been on the increase in parts of coastal Victoria,  and the primary theory is that the virus is transmitted by mosquitoes.


Map of Buruli ulcer risk in Victoria (source: Health Victoria alert 18002).

Not all mosquito species carry diseases of course – in most cases they are just an itchy nuisance; however, it is through monitoring, trapping and laboratory species identification that health officials can spot an impending risk of particular species breeding who may carry these viruses. Through the Atlas of Environmental Health we help DHHS to use visualise the location, clustering and temporal patterns of data regularly collected in the field.

The biggest component of our recent phase of work though has been a new Ground Surveillance Module (GSM) mobile application.  The GSM module – currently being tested – focuses on rapidly inspecting and collecting data on breeding sites at a property level. The app has features and a workflow designed for a minimal click experience – like responsive screen progression, GPS based reverse geocoding (a fancy term for pre-populating a property address), and geotagged photographs.

  
Through simple design the app is getting a neat refresh, which includes reverse geocoding

This GSM app will in future incorporate the adult trapping, larval dipping and public complaint functions currently used in our mosquito monitoring app – bringing the existing functionality into a more flexible and easier to maintain application framework. With mobile technology maturing we wanted to ensure that DHHS was able to take advantage of the new features that are on offer. The most significant of these is parallel platform development for iOS and Android, which results in efficiency savings in development and maintenance.

With the GSM app, local government Environmental Health Officers (EHOs) will be able to capture locations of potential breeding sites through property inspections along with information about whether mosquito larvae are present and whether a treatment was applied. In some cases this would be as basic as removing the water source from a bucket or pot, while in others the EHO may be able to apply a treatment or need to return at a later date.  The rapid entry of data is all about increasing capacity of the EHOs to cover more ground, and to generate a more accurate and timely picture of what is happening across their local area. Larvae breeding in a backyard pond or container typically mature in about 2-3 weeks, after which time a different and trickier treatment type is required, so the app and increased coverage is important for DHHS to manage threats of a disease outbreak. As with risks in most disciplines, if you can identify it early you have more choices about mitigation before it turns into an issue.

 
Simple designs using icons and graphics to streamline data capture is very important for efficient use of the app

If you think about what the EHOs are doing as they visit properties, the rapid data entry gives them time to be more public facing and to engage with people in a useful conversation about preventative measures. They can take the time to show residents and business owners where mosquito breeding can happen, and simple approaches to prevent standing water from turning into a problem. Overturning empty buckets and pots, and keeping pool and pond water circulating over winter for instance, can go a long way to avoid both the unpleasant barbecue experience and serious health problems.

So through this latest phase of work we have added a new app for field data collection and have built an API for connecting the Atlas of Environmental Health to other analytics packages. I think 2019 is going to be an interesting time in this space as we look to solidify these tools and ramp up capabilities in data collection and risk reporting. If you’d like to know more about this topic, strike up a conversation with us on our FacebookTwitter or LinkedIn accounts – or drop us a line on (08) 9227 7309 or email me on chris.roach@gaiaresources.com.au.

Chris

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Environmental Health, Data Standards and Open Source Software https://archive.gaiaresources.com.au/environmental-health-data-standards-open-source-software/ Wed, 05 Dec 2018 01:33:06 +0000 https://archive.gaiaresources.com.au/?p=6288 Recently, I was asked to give a couple of talks to the Indo-Pacific Centre for Health Security (IPCHS) around the Atlas of Environmental Health.  The IPCHS is a relatively new initiative from the Australian Federal Government, which “contributes to the avoidance and containment of infectious disease threats with the potential to cause social and economic... Continue reading →

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Recently, I was asked to give a couple of talks to the Indo-Pacific Centre for Health Security (IPCHS) around the Atlas of Environmental Health.  The IPCHS is a relatively new initiative from the Australian Federal Government, which “contributes to the avoidance and containment of infectious disease threats with the potential to cause social and economic harms on a national, regional or global scale.”  

 My slide deck for the Atlas of Environmental Health.

I attended the two workshops (one in Cairns and one in Melbourne) remotely, saving just under 1 metric ton of carbon.  Presenting remotely is still a bit finicky, with issues around audio and video quality popping up, but not getting on another plane with my travel schedule the way it is seemed like a good tradeoff.  In the end, the presentations worked pretty well, and my slide deck is embedded above.

I try to attend a whole session (so I’m also not interrupting the flow of the talks by dropping in mid-talk), and I got to see a few other talks around other information systems, including some interesting work by the Red Cross Red Crescent Community Based Surveillance software (see the video below), a data aggregation system called Tupaia and some preliminary plans around software development that the Burnet Institute plans to do for their humanitarian work.


The Red cross Red Crescent Community Based Surveillance introductory video

Hearing about all these software systems being created got me thinking, with one point coming up about data standards, and the other about open source software.

Data Standards

The Atlas of Environmental Health has been a collaborative project from day one, working with the Department of Health (WA) and subsequently the Department of Health and Human Services (Victoria).  While we never ended up discussing data standards explicitly while developing the Atlas, it’s coming to the fore now.  This need was highlighted for me during the IPCHS workshops, when you hear about software systems like those above being developed (or already developed) for an area, with no clear way to interoperate.

There are a couple of things often conflated when someone says “data standards” – data standards that are used to store data, and data exchange standards that are used to share data.  In Environmental Health in Australia, both appear to be sorely needed, and this is something that we will need to put some more thought into quite soon – and we will need to gather support from national bodies, like the Mosquito Control Association of Australia and the National Arbovirus and Malaria Advisory Committee, two peak bodies in this mosquito control area.

Open Source

Over time, I’ve heard quite a few groups conflate “open source” with “interoperable”.  Just because your software is open source doesn’t mean it works with everyone else’s software, and it doesn’t mean that a bunch of bored software engineers will descend upon your codebase to work on it.  This topic was covered pretty well by Paul Ramsey in his FOSS4G keynote – linked in our last blog.

Open source software is something we’ve specialised in, and, like our work in citizen science, the success of these ventures is all about engagement and support.  If you don’t have a strategy around engaging and working with potential software engineering volunteers, then you won’t suddenly get a bunch of people working on your software – just putting it out as open source does not guarantee anything.

If you open source it, they won’t (necessarily) come.

There’s a lot more to be said around these topics, and that’s something for another blog down the track – I have been looking around at environmental health data standards for the last week or so (yes, while on holiday) and I think a separate white paper is in order… stay tuned.

For more information on the Atlas or data standards, drop me a line via email (piers.higgs@gaiaresources.com.au) or start a conversation with us via  Facebook, Twitter or LinkedIn.

Piers

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