TDWG (“tadweeg”) is a great acronym and best explained from their own web site (www.tdwg.org):

Historically known as the Taxonomic Databases Working Group, today’s Biodiversity Information Standards (TDWG) is a not-for-profit, scientific and educational association formed to establish international collaboration among the creators, managers and users of biodiversity information and to promote the wider and more effective dissemination and sharing of knowledge about the world’s heritage of biological organisms.

Unlike what the local cafes thought (hats off to The Stagg for this one) , it’s not a taxidermy or really even a taxonomy conference: it’s about biodiversity data and standards around that data – and it attracts people from all over the world.

What I found really amazing was not only the efforts that the organisers put into making sure the hybrid conference worked for both in-person attendees and those attending virtually, but the range of interesting and thought provoking papers that were presented.

It’s always hard to come up with a summary of a conference that goes for a week and involves a lot of thought provoking stuff – I mean, I’ve got about twenty pages of notes to work through – but Mieke and I are giving it a go for our team, so here’s the recap of that recap!

Firstly and we’ve got to claim our own stuff as a highlight – but both Mieke and I gave talks this year.  Mieke was talking about translating between the Darwin Core data standard and the Australian Biodiversity Information Standard, and this is a key part of the work we’re doing helping the Department of Climate Change, Energy, the Environment and Water deliver the Biodiversity Data Repository.  Meanwhile I was presenting on the work we’ve done on the Restricted Access Species Data (RASD) Service with the Atlas of Living Australia. Note: we’ll update this blog in the future with the recordings when they become available.

The themes that we saw at the conference that really stuck with us included:

• Data quality – a bunch of talks about data quality made us really agree that what defines quality is case dependent on the end user needs.  Having some “fitness for purpose” flags (e.g. suitable for modelling) that can be associated with them – this is far more nuanced than the usual “good quality” tags.
• Integration – there were talks on a range of systems like taxonomic backbones, data repositories and other systems – there are a lot of opportunities to synthesize and aggregate data, as well as connect to some significant infrastructure services that can really help with standardisation and connectivity between data sources.
• Terms of useMore and more fields – with the RASD workshop, we also saw some great talks about both the FAIR and CARE principles that really have given us food for thought.  These principles – RASD, FAIR and CARE – all provide frameworks for how to format data so that there are appropriate levels of access depending on the content and context.  Adding in some additional fields not only to the data stores that we work with, but also the data exchange methods we use, will certainly add a lot to the accessibility and meaningfulness that’s out there in biodiversity data space.
• Artificial Intelligence is out there and being used – we already knew this, but it was great to see a wide range of pragmatic and useful ways in which AI can assist in the efforts across the biodiversity community to solve some big challenges – digitisation, transcription, data processing, identification and data indexing just to name a few!  

One of the big things we did differently this year was to help out and support the first ever TDWG Student Prize.  This is a really important thing to do – supporting our students is the way to make sure that we’ll have a thriving and active community moving forward.  So it’s really important to support our students, and congratulations to Michael Elliott for taking the prize home, and for all the students who were part of the conference.  

Any conference is not without a lot of side-bar (or maybe front-bar) talks and Hobart put on a great show for us.  We were able to get out and try a bunch of different places with colleagues and friends – we can definitely recommend the Blood Orange Stout from Custom’s House.  Hobart is a great place to visit (I’ve been there a few times now) and will be back again in the future as well.

So finally, a big thanks to all the people that made it happen, both in person and virtually.  TDWG is pretty unique – it’s a conference that ticks two of my great loves of technology and biodiversity – and I’m really hoping it won’t be another 15 years before I get to another one!  If you want to know more about any of the topics touched on in this blog then drop me a line, or start a conversation with us on social media Twitter, LinkedIn or Facebook!

Piers

The post TDWG 2023 appeared first on Gaia Resources.

On Wednesday 9 December, Chris Roach and I attended a webinar hosted by the Atlas of Living Australia (ALA), celebrating its 10 years of existence and showcasing research into the role of Big Data and data science modelling techniques in managing Australian biodiversity. It was a chance for me to also reflect on my journey in parallel with the ALA in the early days when I was at the Western Australian Museum. I was involved there in aligning the Arachnology database fields with the TDWG Darwin Core standard, so the web team could mobilise our data; then later in environmental consulting; and now here at Gaia Resources where we share much of the ideals of the ALA in enabling open biodiversity data sharing and aligning to internationally recognised standards.

The following provides a summary of some of the important research that was described in this particular seminar series of three speakers.

With platforms such as the ALA, the amount of biodiversity data available has dramatically increased in the last 10 years and empowered biodiversity conservation with so much more confidence in actions undertaken; but many of the ecological challenges that we have faced in the past still remain. These challenges can be summed up in three main areas:

• Sampling bias,
• Incomplete coverage and,
• Data quality.

Professor Melodie McGeoch (La Trobe University) discussed the importance of not just focusing on documenting populations of threatened, vulnerable, and endangered species; but also the need to recognise the importance of occurrence data for “common” species. Whether a species is recognised as common depends on temporal trends, local abundance, and spatial range; and significant declines in any of these areas may go unnoticed when a species is thought to be common enough not to require frequent monitoring. In terms of identifying refuges for preventing diversity and biomass decline, Prof. McGeoch advocated for the modelling of ALA and other data of both rare and common species at a more localised level to understand geographic variation and abundance over time.

PhD candidate Tianxiao (August) Hao (University of Melbourne) used his research in fungal diversity in Australia to show the rapid increase in data availability. Some of this data, however, is unreliable, and so careful consideration must be taken prior to analysis as to whether the data is of a high enough standard to be useful. He acknowledged the new technology and rigorous screening that new data submitted to the ALA undergoes and the large clean up operation that is underway to increase the quality of legacy data.

Both August and Professor Jane Elith (University of Melbourne) demonstrated how the available data is still biased greatly by sampling effort due to environmental or logistical constraints. It makes sense that the easiest to reach places, such as areas near population centres, coastlines and, along roads are the most heavily sampled.

Professor Elith also highlighted the much forgotten bias introduced by a deficiency in absence data. Most ‘observation’ records are for presence data, but having knowledge of what areas have been sampled (and how) without finding occurrences, is possibly of equal significance to documenting the presence of species. Predictive modelling of species distributions are so much more powerful when they can account for bias and ideally this presence-absence type of data capture should be integrated into research and citizen science initiatives.

Professor Elith showcased the eBird initiative as a good example of where using citizen science can provide comprehensive coverage of occurrence data over time.

Gaia Resources is no stranger to considerations of presence-absence data and has developed several Citizen Science solutions over the years. We have also worked with conservation groups like the Great Victoria Desert Biodiversity Trust to plan habitat survey strategies (check out our blog here).

With the help of open-access biodiversity data such as that provided by the ALA, we can all play a part in overcoming the challenges faced in conservation. Here’s to the next 10 years!

If you’d like to know more about this topic or would like to discuss your own Big Data and biodiversity projects, please drop me a line at mieke.strong@gaiaresources.com.au, or connect with us on Twitter, LinkedIn or Facebook.

Mieke

The post The ALA and Big Data for Biodiversity appeared first on Gaia Resources.

There was a fine range of symposia and discussion sessions to choose from. These annual conferences serve two purposes:

• to provide a forum for developing, refining, and extending standards in response to new challenges and opportunities; and
• to provide a showcase for biodiversity informatics – much of which relies on the standards created by TDWG and other organizations.

Data standards that describe and support the exchange of biodiversity information are critical scientific infrastructure. They enable data to be integrated in support of research, decision-making and conservation planning. Ultimately, standards extend the usability of data across taxa, scientific disciplines, and administrative boundaries.

Gaia Resources now has a long history of actively participating in TDWG. Having attended my first conference in Reading, UK in 1998, I became the Oceania representative from 2002-2008, and in the year I took my leave from that position Gaia Resources played a major role in helping host the conference in Fremantle, WA.

This year a small team here prepared an interesting case study for presentation in the conference session entitled “Avenues into integration: communicating taxonomic intelligence from sender to recipient”, organised by researchers from Arizona State University. Serge, Kehan, Jason and I worked on exploring ways of validating taxonomic names data embedded within environmental impact assessments and survey reports. This was spurred by two initiatives:

• the availability of a new and improved taxonomic names interrogator – GNfinder, that significantly improves the speed of finding and retrieving taxonomic name strings from a document with references to the Global Names Index, and
• the availability of IBSA – an open repository of environmental surveys in Western Australia.

The result was a small prototype we called ‘Species Informer’.

We created a procedure for uploading PDF documents, analysing taxonomic names, and then interrogating the Atlas of Living Australia for ancillary data for those names, such as local conservation status, in order to provide an automated summary of taxon names issues within each document for further analysis. We also ran a small test on image-only data using AWS Textract, to extract text from documents scanned as images to use as well.

Preliminary findings, from a small sample, included:

• gnfinder speeds the process of finding taxon names uttered in a document
• of course, it finds all taxon name mentions, not just the relevant ones for the survey
• we didn’t explore the gnfinder options for sensitivity, data source or context searching
• Species Informer produces a CSV report in c. 1 minute, as opposed to perhaps 8 hours for manual verification
• at a c. 90% success rate for finding taxon names in a report, environment officers still need to check the whole document
• not currently included in the Global Names Index are ‘phrase name taxa’ – c. 7% (1,143 of the 15,558) of the native vascular plant taxa in WA, and c. 15% (558 of the 3,782) of conservation taxa.

Some primary conclusions from this study included that ‘data governance’ is required at all parts of the process:

• preparing the source report to ensure all taxa are resolved
• the taxon names available to the Global Names Index could be expanded to include authenticated unpublished (phrase) names
• the regular maintenance of name currency, conservation status and child taxon information is necessary
  conservation status needs to be better maintained at regional, national, global levels.

The video of is now available so you can hear the presentation and see the detailed results of our study. In fact, I would commend all presentations for viewing as many innovative methods for communicating taxonomic intelligence from sender to recipient were presented.

If you’d like to know more about this project, please drop me a line at alex.chapman@gaiaresources.com.au, or connect with us on Twitter, LinkedIn or Facebook.

Alex

The post TDWG 2020 Conference – avenues into integration appeared first on Gaia Resources.

Data standards that describe and support the exchange of biodiversity information are critical to scientific infrastructure. They enable data to be integrated in support of research, as well as decision-making and conservation planning. Ultimately, standards extend the usability of data across taxa, scientific disciplines, and administrative boundaries.

Current and previous TDWG data standards

The annual Biodiversity Information Standards (TDWG) conferences serve two purposes:

• to provide a forum for developing, refining, and extending standards in response to new challenges and opportunities; and
• to provide a showcase for biodiversity informatics – much of which relies on the standards created by TDWG and other organisations.

Gaia Resources has been involved with this international standards body for some time, either utilising their data standards in various projects, developing modules for TDWG itself, or actively participating in their standards development.

While with the Western Australian Herbarium, I and other scientists worked on a number of TDWG standards (notably HISPID, ABCD, SDD and DELTA) and was the Oceania representative of TDWG for 6 years, culminating in hosting the 2008 annual conference in Fremantle, part-sponsored by Gaia Resources and Piers a valuable organising committee member.

This year’s virtual conference will be scheduled the week of October 19-23 and some of our team will be participating in various sessions. I would commend attending this conference if you’re keen to keep up with the latest work of this dedicated global community.

If you’d like to know more about Gaia Resources involvement and use of biodiversity information standards then please drop me a line at alex.chapman@gaiaresources.com.au, or connect with us on Twitter, LinkedIn or Facebook.

Alex

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Yet, it has traditionally been the scientific paper that takes precedence as the vector for knowledge, with its core data relegated to a few tables locked into print format. The bulk of the collected data is left in lab books, spreadsheets and analysis software formats in the scientist’s office, or at best as supplementary digital data tables on the journal’s website.

What happens at the two ends of a scientific project can be the most critical. Once a ‘research question’ has been proposed, defining what data must be collected and the methods that ensure rigour and accuracy of recording data become paramount. Poor project design can kill a project. Likewise, once ‘the paper’ is out, where does the data go?

Data capture is increasingly being aided by automation, such as sensors that measure one parameter accurately, repeatedly and automatically submitting the data points to the scientist digitally. Smartphone apps are now commonly used to improve the accuracy of observations by providing their users with accurate automated data on geo-location and date/time, as well as controlled vocabularies for each form field.

Submitted data is then stored in a project data repository where administrators can vet, validate, curate and download data for further analysis. While the project is active the data is maintained; but, once the paper is out and the research funds dry up? In the figure above, the ideal ‘life cycle’ is illustrated.

Nature Science Data provides a best practice model for projects that result in a scientific publication. It mandates the release of datasets with accompanying Data Descriptors, instructs authors to submit datasets to an appropriate public data repository, and maintains a list of vetted data repositories.

To make the data maximally retrievable and reusable, (globally) agreed data standards are crucial. One example from the biological realm is the Biodiversity Information Standards (TDWG), a non-profit scientific community dedicated to developing biodiversity data standards.

In my neck of the science woods, herbarium and museum collections provide an excellent long-term store of absolutely raw data, in the form of a preserved specimen from which multiple researchers over time can extract useful data. With the digitisation revolution in recent decades this fundamental biodiversity has been captured and liberated through institutional websites (eg. FloraBase – the Western Australian Flora) and federated to provide national (Atlas of Living Australia) and global (Global Biodiversity Information Facility) data portals.

For example, as part of UWA’s honey bee project I scored phenological data for a eucalypt species complex using Access to Biological Collection Data (ABCD) standard fields. This data was appended to metadata in the WA Herbarium’s specimen database to become available to researchers around the world.

So, a clearly conceived Data Management Plan should be essential for any scientific research and Citizen Science projects are no different. However, CS projects commonly have a very low funding base, run for just a relatively short period and may be related to a single researcher’s project for which the outcome is a thesis or paper. If a project ends and the digital datasets are not adequately archived in a useable format in a major searchable repository then that hard-won data cannot be maximally discoverable and re-usable.

A good fall-back in this situation would be to at least lodge the data and metadata in the Australian National Data Service (ANDS). ANDS aims to make Australia’s research data assets more valuable for researchers, research institutions and the nation. The site contains many guides to standards, methods and contribution – and is well-worth referring to when considering your next research project.

If you’d like to know more about how we can help you with developing a citizen science program, please leave a comment below, connect with us on Twitter, LinkedIn or Facebook, or email me directly via alex.chapman@gaiaresources.com.au.

Alex

The post The Data Challenge for (Citizen) Science appeared first on Gaia Resources.

I can now – very proudly – announce that we caught them!

The process of getting to this point has been a pretty intense one, especially for those of us that are on our Quality Team – Shay and Drew as our Security Officers, Gill and Barb as our Quality Managers, and Andrew and myself as the ‘Risk Owners’. Other staff also played a role in getting us here and in the last few months we’ve been steadily rolling out a whole range of improvements to our procedures and working practices.

We realised this morning that, with new appointments coming on board recently (and introductions are coming shortly), that we almost number 30 staff – the biggest that Gaia Resources has ever been. And this is one of the reasons that the Quality and Information Security Management Systems are so important. As I mentioned in that previous blog, it’s important that we enshrine our standards in procedures and processes that enable us to continue to deliver high quality solutions to our clients.

One of my favourite parts of the ISO Quality System is the ‘Opportunity for Improvement’ (OFI) component, that empowers anyone within our organisation – or even our clients – to suggest ways in which we can improve our procedures and systems. This was an initiative we’d already taken at our strategy workshop earlier in the year, but formalising the procedure really does add some more weight to it. We have a lot of OFIs already being implemented as a result of our audits and certification process, with more to come.

And so, to reiterate what I said in the previous blog, if there’s some way that you think we can improve what we’re doing (i.e. an OFI!), we’d love to hear from you. Please drop me a line directly at piers@gaiaresources.com.au, or start a conversation with us on social media via Facebook, Twitter or LinkedIn.

Piers

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Perhaps you enjoy spending your leisure time in nature? Does playing games online strikes your fancy? Are you thrilled about another activity or cause? Do you love science communication?  Perhaps you are considering exploring citizen science as an avenue to follow your passions, but where do you start? Before you dive into creating a new group or project, it’s worth exploring what groups, resources and projects already exist.  If you haven’t found the prefect project to jump straight into and you are game to create one, then it’s worth considering if there are already online platforms that can assist you with your project – and I have seen quite a few of the platforms around the world from the #CitSci2019 conference!

If your project involves collecting observations of nature and then entering them online, the citsci.org platform offers this functionality for projects in the United States. The citsci.org leaders also ran symposium that explored funding models of different organisations running large scale projects. The room was absolutely packed, which clearly demonstrated to me the struggle we all have with sustainably funding long-term projects!

"Exploring Sustainable Funding Models for #CitizenScience" #CitSci2019 Symposium was packed yesterday! I think this speaks to #citsci funding struggles being ubiquitous. Nice job Greg Newman & Russell Scarpino (@CitSci), Luigi Ceccaroni (@Earthwatch_Eur), & Dixon Butler (@ylaces) pic.twitter.com/0Y0sd28kQF

— Jessie Oliver (@JessieLOliver) March 16, 2019

If you are interested in kicking off a project that entails online tasks, such as transcription of datasheets or classification of media such as images, audio, and video, then it’s worth checking out the project builder on the Zooniverse platform. The Zooniverse currently hosts nearly a hundred online projects focused on several areas of science and some even overlapping with humanities. I was thrilled that #CitSci2019 gave me the opportunity to learn more about this platform in the context of my own technology design research on how to design engaging technologies to search environmental audio recordings to find Eastern bristlebirds.

A sample prototype page from Jessie’s research that she shared during her talks and networking

Of course, Gaia Resources has also been developing their own citizen science toolkit, called Project Hydra, and has used this to deliver many citizen science apps like these.  The nearest Australian equivalent is the BioCollect platform developed by folks with the Atlas of Living Australia, which is a biodiversity data repository.  The Gaia Resources team (especially Piers and Alex) are keeping an eye on all the platforms that are out there and can certainly help advise people on the available tools.

What if existing tools and platforms don’t do what you need?  If you have a vision for a project, but you don’t have access to the technologies needed to make your project a reality then there is nothing to stop you from starting – time to get brainstorming!

There is a lot of talk within the citizen science community about the strategies of citizen science project design strategies, and it’s certainly important to consider what strategy is best for your project idea and your anticipated community. Most projects in Australia are led by scientists and engage citizen scientists to contribute data or analysis skills. Another less common but important strategy is when projects are driven by members of the public who then recruit scientists to contribute expertise to ensure a project is developed in a scientifically rigorous way. Other projects are also cooperatively created, or co-created, with scientists and community members working together from the start.

As you begin to think about technological needs, it is similarly important to consider who is going to be involved in creating technologies, at what stages, how, and why. Typically, technologies for citizen science are often envisioned by scientists who have the aim of solving specific scientific riddles. If scientists are creating technologies in isolation, focused on their scientific objectives, they may not always be well positioned to determine whom might use their technologies, as well as where, how, and when. Are scientists well positioned to study people’s practices, tech use habits, or hobby motivations well beyond the science? Sometimes, sure, particularly if we are talking about social scientists and anthropologists; however, scientists focused on solving ecological woes may not always have time or knowledge to study people’s requirements too. Conversely, community members without any scientific training may not have the background to inform developing technology in ways that will lead to scientifically rigorous outcomes. So, what is a person to do?!

This is where technology designers can help! Folks like myself, trained in Human Computer Interaction (HCI) design, can work with both scientists and community members to explore alignment of interests and goals. Contrary to what most people imagine when I describe my work in technology design, I spend my days studying people, often taking an ethnography research approach with a high level of empathy, to understand people’s practices, motivations for activities, technology use, and more. Most people start considering questions such as:

• Does my project idea require field devices to complete tasks or collect data?
• Does my project need an online data portal?
• Does my project require a mobile application?
• What should such technologies look like?

Before diving into these questions too deeply, however, I typically take a bit step back and consider a different suite of questions first, including:

• Who do I anticipate will be core contributors to a project?
• What evidence do I have to support this?
• Is there a way we could understand this better before creating anything?
• How can existing practices of anticipated participants inform the design of project technologies?

Beyond creating new projects, it’s also important to consider how existing technologies like application and website interfaces might benefit from a facelift. I am particularly keen to also help folks explore re-designing existing technology iteratively (i.e. design, evaluate use, improve design, re-evaluate, repeat). To do this I come from a slightly different angle, working with folks using the technologies to identify barriers to use, ways to extend accessibility, techniques to enhance short and long-term use integration, reaching citizen science groups, and more.

This is the sort of role that we have been discussing for Gaia Resources, to bring my HCI expertise (and of course, Morgan’s accessibility expertise) into the future of the citizen science offerings from the company.  It will be exciting times (when I get back to Australia!).

Now we have a platform designed and technologies chosen, how do I make sure my project’s data is useable for others?

Welcome to the exciting world of data and metadata! Don’t know the difference between the two? Yeah, neither did I until a few years ago.  If you would like more information, this blog from some of our European colleagues does a pretty good job at breaking down data, metadata (data about data), the importance of standardising data, and the ability to exchange data between different databases (i.e. data interoperability).

Groups around the globe are working together to create standards for citizen science data to maximise its usefulness, and to ensure data can be exchanged between the different databases around the world. Being involved in these discussions for several years now, I attended several meetings, talks, and workshops related to advancing these efforts. Stay tuned as this diverse group is currently exploring how to get more information out there to everybody.

Co-chairs Greg Newman (left) and Justin Schell (left) leading a discussion on data and metadata

What if other people are investigating the same general topic, but using different methods?

It’s an ideal scenario for creating an online ‘one-stop-shop’ for people to find and discuss a suite of methods being used. Then newcomers can also explore what methods are out there and most likely to work in their respective regions with a given population of people. If the methods shared need some tweaking to work in a new region or with new people, than iterative adaptations can then be shared back into the group for others to use.

It is this idea that is the basis of the developing consortium called Global Mosquito Alert, which aims to bring mosquito monitoring citizen science methods together.  Over the last few years, I have looked to understand what mosquito monitoring projects engage citizen scientists and how in Australia, and have liaised between those groups and the global consortium. While at #CitSci2019, I was asked to join a panel discussing how the Global Mosquito Alert consortium folks exchange knowledge, and how the consortium are likely to work with the develop Citizen Science Global Partnership and Earth Challenge 2020 initiatives.  It’s wonderful to see so many people working together from around the world to harness technology to increase the impact of citizen science!

If you are interested in more discussion about citizen science and technology, don’t hesitate to let me or other folks at Gaia Resources know (via their social media channels or directly through to Piers or Alex).  We’ve got plans afoot at Gaia Resources around technology and design that Piers and I will be discussing when I am back from this trip so stay tuned for more from us on technology and citizen science!

Jessie

The post Choosing technology for Citizen Science appeared first on Gaia Resources.

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.

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 Facebook, Twitter or LinkedIn.  I’d like to hear what you think, and how we can compile more resources on this!

Piers

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There are a range of use cases that we can expect will be relevant for the future, like:

• what species and ecological communities occur in this parcel of land and how complete and reliable are those data?
• how representative is our biodiversity knowledge in any location and across the State?
• where are all the long-term survey sites and what can they tell us about the changes in biodiversity and ecosystem health over time?
• what are the ecological constraints on any new land use proposals?

What data do bioinformaticians need to provide to clients and decision-makers to meet these use cases?  As ever – it starts with ‘what and where’ in a variety of ways:

• what populations, species, assemblages, ecosystems, and where do they occur;
• what are the risks and threatening processes to be considered and where are those risks at there highest;
• what are the gaps in our knowledge and where are the skills and resources required to fill those gaps.

One example of the types of ‘what and where’ that will be asked can be shown in some of my research and development projects that I have been working on over the years, like this example for the Western Australian Herbarium collections, illustrated below.

This web tool displays c.510,000 geocoded specimen records from the Western Australian Herbarium faceted
by 438 plant families, along with a summary of their collection dates by decade and pop-up links to FloraBase

While it is currently possible to interrogate individual systems (as above), or DBCA’s NatureMap, or utilise national data aggregators such as the Atlas of Living Australia, to develop a comprehensive approach within the State we will, at a minimum, require:

• layers of web services implemented on top of existing data systems in order to make core data available across domains,
• a portal to visualise the available data with ‘dashboard features’ to quickly provide metrics on the biodiversity of an area and representativeness / completeness of that data,
• a long-term plan for building infrastructure and connectivity with a strategic plan for increasing and improving the data in the system, and the systems themselves.

The first steps will potentially be:

• a stocktake of all the relevant information systems;
• detailed analysis of those system schemas and the applicable data standards in use;
• modelling of the data interactions to flexibly deliver the key use case functionality;
• implementation of any required changes to individual data systems to enable full participation in the new system;
• identification of system dependencies or weaknesses to ensure each contributing information system can continue to reliably deliver.

Demand for biodiversity knowledge is increasing. There are many projects aiming to deliver new information — effective and efficient coordination across all stakeholders will be key. If you’d like to talk further about future initiatives, contacted me directly via email (alex.chapman@gaiaresources.com.au), or through Facebook, Twitter or LinkedIn.

Alex

The post Biodiversity informatics future requirements appeared first on Gaia Resources.

To present FloraBase to that audience was a special moment – one of the first herbaria to have their entire collection online, and in one of the world’s 35 biodiversity hotspots. It had taken a lot of hard work – some of that is described in the Landscope article published this week to recognise the 20-year milestone for the FloraBase site, co-authored with herbarium colleagues John Huisman and Ben Richardson.  Crucial to this work was the:

• creation of a specimen database to house the State’s herbarium collection documenting, via specimens and label data, the plant biodiversity and distribution across the State. Started by Curator John Green in 1985, I took over the management of WAHERB in 1989; the collection was fully databased by 1994 and maintained subsequently;
• development of the State’s vascular plant census, published in print in 1985, but converted to a proper database format by Nicholas Lander, and then implemented in its current form (WACENSUS) by Paul Gioia and I from 1990 onwards;
• Descriptive Catalogue project, developed between 1993 and 2000 when it was published in hard copy and incorporated into FloraBase to provide simple identification and descriptions across the whole flora – some 11,922 taxa occurring in the State at that time — it was maintained and updated for a further eight years;
• development of curated images to illustrate the habitat, habit and diagnostic features of each taxon — all achieved through a large citizen science effort primarily from the WA Wildflower Society volunteers; and
• automated and regular calculation of simple distribution maps for each taxon.

An example taxon profile page illustrating the aggregated elements (names, images, specimen map and a description). FloraBase continues to be heavily used since the launch in 1998 (and relaunch in 2003)

By positioning the specimen, names and image databases right within the curatorial purview of the WA Herbarium, and providing useful tools for the curators and scientists, the systems were quickly adopted. Many curatorial processes were realigned or adjusted to incorporate the databasing procedures, and once the World Wide Web came into existence in 1994, the development of FloraBase on top of these existing systems was a compelling enhancement.

After my stint as ABLO and the launch of FloraBase and the early AVH versions, I became further involved in the development of international data standards as the Oceania Secretary of Biodiversity Information Standards-TDWG  in 2002 and attended a number of international meetings to develop the Access to Biological Collection Data – ABCD – a global schema to allow all biological collections to be shared and aggregated.  These two data standards projects were crucial to the development of the Global Biodiversity Information Facility – GBIF and shortly thereafter, the Atlas of Living Australia – ALA.

Back in WA, FloraBase 2.0 was launched in 2003, with major functional improvements and the State’s systematic botanical journal Nuytsia, of which I had been the editor for a number of years, also became part of FloraBase.

I had seen work that Gaia Resources had been involved with, such as building an ImageBank solution for the WA Herbarium to manage over 50,000 taxon images and their relationship to name and identification changes. They also implemented the first data engine for the ALA to manage and integrate species data from a multitude of contributing source, and to initiate management of their citizen science interactions.  When I moved on from the WA Herbarium, joining the Gaia Resources team was the best next step to help guide their work on the State’s biodiversity informatics infrastructures. Two relevant early projects were the:

• construction of a single home for the WA Museum‘s many disparate specimen collections databases; and
• initial implementation of a unified collections management system for the CSIRO’s National Research Collections.

Flip forward to 2018 – and all the systems mentioned (apart from the two above), though innovative in their time, are now ageing and in need of replacement. At the same time, the world has moved into the era of big data, where smart tools can work over large-scale aggregated data sets to allow mere humans to deduce appropriate actions.   While the fundamental curated datasets are irreplaceable, new technologies must be put in place to enable their continued longevity. Data standards must be utilised to help aggregate data to a State level to enable agencies such as the Department of Biodiversity, Conservation and Attractions (DBCA) or the Department of Water and Environmental Regulation (DWER) to get on with its work on conserving and managing the State’s biota.  Initiatives such as the WA Biodiversity Science Institute – WABSI are heavily involved in supporting this sort of work.

Recent Gaia Resources work on creating a flexible data repository for State agencies’ biodiversity data (see last week’s blog about our work with the DBCA on Biosys) show the way forward for flexibly storing ‘big’ biodiversity data.

A new generation of data management and systems integration is required today to enable effective dissemination of biodiversity data across multiple agencies. Decision-makers require the best-available information to hand in order to make good decisions for conserving the environment.  New methods enabling such critical analysis must be envisioned while ensuring the critical core information systems continue to be upgraded and maintained into the future.  One recent excellent example of such new tools is the Threatened Species Recovery Hub’s Australian Threatened Bird Species Index.

As was alluded to last week, we’ve been brainstorming ways in which that can happen here at Gaia Resources – which I’ll blog about in the new year – and we stand ready to help achieve these crucial tasks.  As always, we can be contacted directly via email (alex.chapman@gaiaresources.com.au), or through Facebook, Twitter or LinkedIn.

Alex

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The latest Brisbane Website Accessibility and Inclusive Design Meetup

After a long hiatus, we held our first Meetup in almost 1.5 years on Thursday 7th September, where I gave an overview about the changes in WCAG v2.1 (Website Content Accessibility Guidelines) compared to v2.0.  The WCAG are part of a series of web accessibility guidelines published by the Web Accessibility Initiative (WAI) of the World Wide Web Consortium (W3C), the main international standards organization for the Internet, and they’re the standards we work towards to make websites more accessible primarily for people with disabilities – but also for user agents and devices like mobile phones.

In short, WCAG 2.1 hasn’t changed a whole lot, with 3 new guidelines (2.5, 2.6 and 2.7),  4 new success criteria for Level A compliance,  9 new success criteria for Level AA, and two new criteria for AAA. I should say, this is all based on the draft guideline released in August 2017, so the numbers may well change with future drafts.   Version 2.1 isn’t really a whole different, despite the 10 years between versions. 2.1 really aims to fill some gaps in the standard, rather than re-imagine website content accessibility; so will be interesting to see how that evolves and if Version 3.0 is around the corner that may incorporate more WAI-ARIA (Web Accessibility Initiative – Accessible Rich Internet Applications) suggestions.

If you’re going to talk accessibility – may as well make your presentation accessible too!

If you’d like to grab a copy of my presentation, I’ve exported it a PDF and you can get plain text accessible version of the presentation from my website. This will explain more details about the changes.

A big thanks goes to our hosts the Console Group, who provided a venue, drinks and food, and organised live captioning for the event.  The Meetup will be monthly, and we’re already planning October’s event – get in touch with me directly if you’d like to know more!

Morgan

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A screenshot of our Citizen Science Project webmap

This project webmap provides a spatial representation of the areas where these projects are focused (e.g. if it’s a state based project, the project ‘pin’ is the centre of the relevant State, or country, or even the planet), their broad topic (marine, terrestrial, or both) and a link to more information about the project. The project map complements the data map already in our Citizen Science Hub, that shows the data points collected across all our projects (which you can see underneath the Projects map, again via this link).  We’re once again using our GRID system to store the locations of the projects, but this time Andrew has put together a specific Leaflet plugin in the Citizen Science Hub that will visualise the points the way that we want them to be visualised (e.g. by the category and the size components).

One aim of this was to collate data on where our Citizen Science Hub projects are located, so that we can help people to find local (or even global) citizen science projects that match their interests. Given our background of working with standards-based methods, we also wanted to document this diversity of projects using a standard, and so we used the Public Participation in Scientific Research Core (PPSR-CORE) metadata standard (which you can read more about here).

Each of the projects in our Citizen Science Hub were cataloged using the PPSR-CORE standard.  However, the names for these fields aren’t really user friendly, so we’ve used aliases to display something a little more readable.  For example, instead of ProjectGeospatialRange, we use “Scale”.  This is something that often happens with data standards, in that colloquial names will emerge for the complex, machine readable, field names.

In the meantime, we’ll keep adding more citizen science projects to the map as we have more active participants in the Citizen Science Hub.  If you are interested in participating in one of the projects, or starting your own, then contact us via the Citizen Science Hub, leave a comment below, or start a conversation with us on Facebook, Twitter or LinkedIn.

Tracey, Andrew and Alex

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