Shared Vocabularies Create Oceans of Opportunities

Climate science, Environmental management and policy, Environmental sciences and technologies, Information and computing sciences, Language - communication - culture, Marine research and ocean industries

Research vocabularies are helping researchers aggregate data from a wide range of sources and disciplines to find evidence-based solutions to big societal challenges such as climate change.

In 2021, an analysis of sea temperature data collected from the Southern Ocean over 25 years revealed disturbing evidence that the potential for Antarctic ice-sheet melting has been hugely underestimated in past studies. The resulting sea level rise could have dramatic impacts around the world.[1]

The unique time series of data was collected on board the French Antarctic resupply vessel L’Astrolabe, from 1992 to 2017, between Hobart and Antarctica.

It’s not unusual for scientific institutions to use volunteer merchant vessels to routinely gather observations. Known as ‘ships of opportunity’, they are a cost-effective way of collecting multidisciplinary oceanographic data for measuring the speed of change in the marine environment.

This map was sourced from the AODN portal supported by Australia’s Integrated Marine Observing System (IMOS) – IMOS is enabled by the National Collaborative Research Infrastructure strategy (NCRIS). It is operated by a consortium of institutions as an unincorporated joint venture, with the University of Tasmania as Lead Agent.
This map was sourced from the AODN portal supported by Australia’s Integrated Marine Observing System (IMOS) – IMOS is enabled by the National Collaborative Research Infrastructure strategy (NCRIS). It is operated by a consortium of institutions as an unincorporated joint venture, with the University of Tasmania as Lead Agent.

Taking the Ocean’s Temperature

CSIRO data analyst and scientific programmer Ms Rebecca Cowley manages the Integrated Marine Observing System (IMOS) Ships of Opportunity program and is responsible for quality control and for sharing the data with other institutions.

CSIRO is part of the consortium that operates IMOS, which is enabled by the National Collaborative Research Infrastructure Strategy (NCRIS).

To record the ocean temperature, IMOS uses expendable temperature probes, which are deployed overboard at regular intervals. Attached to a long copper wire, the probe can sink to about 900 metres, and sends temperature data up the wire at various depth intervals, to an on-board system.

Within minutes, Ms Cowley can review the data from her office in Hobart and share it with the Global Telecommunication System (GTS), a global network for the transmission of meteorological data.

Within hours, the data is available to weather bureaus around the world, for use in climate modelling and forecasting, and is automatically added to Australia’s marine and climate science portal, the open access Australian Ocean Data Network (AODN). All this, with minimal human intervention.

Using a Common Language Speeds Up Data Sharing

A crucial part of what makes this machine-to-machine data sharing possible, streamlined and fast is the agreed research terminology, defined in ‘research vocabularies’, which institutions share and adhere to for describing collections of data – both the metadata and the data itself.

A vocabulary can be used to annotate data unambiguously; for example, the data must be attributed to the correct ship, so the name of the ship or its unique ‘call sign’ must already be registered in the AODN Platform Vocabulary or the data transfer will fail.

Vocabularies Support Data Discovery and Aggregation

A research vocabulary can be as simple as a glossary or a list of codes that anyone in the research community can add to. Others, such as units of measure, taxa and rock types, are tightly controlled. The minimum requirements for a useful vocabulary are a unique label and a description or definition for each term in the list, though increasingly they also contain synonyms, intra-vocabulary relationships and cross-vocabulary mappings.

From plant taxonomy to disease classification, science depends on precise language and referencing. Finding evidence-based solutions to the grand societal challenges of this century requires that scientists use shared scientific concepts to pool their work. This enables them to aggregate vast amounts of data from multiple sources, often from multiple disciplines and domains, and from countries where differing languages are spoken. Clearly, unless a data collection is tagged using globally agreed terms, it cannot be part of the global web of information systems necessary for tackling challenges such as climate change.

Vocabularies Are Best When They Are FAIR

Like research data, research vocabularies are best when they are FAIR – findable, accessible, interoperable and reusable.

The ARDC provides an open, web-based service for publishing and accessing vocabularies. ARDC Research Vocabularies Australia is designed for people who support, describe and discover research – such as vocabulary managers, ontologists, data managers and librarians – and for researchers. It helps them create, maintain, find, access and reuse research vocabularies.

Several institutions host their vocabularies directly on ARDC infrastructure. Others are linked to on their home websites.

As of this year, 484 research vocabularies are openly shared on Research Vocabularies Australia by 87 registered publishers, including IMOS, TERN, Geoscience Australia and the Australian Bureau of Statistics. More than 100 people from research institutions are registered vocabulary contributors.

Some of the most heavily accessed vocabularies are a ‘fields of research’ vocabulary, a public policy taxonomy, an astronomy thesaurus, and an index of psychological terms.

158 of these vocabularies come with a readymade tool, or ‘widget’, which users can ‘plug in’ to their own data capture tools, allowing them to draw directly from ARDC-hosted vocabularies to classify their data.

An independent evaluation by CSIRO of Research Vocabularies Australia in 2019 found that it “is meeting a clear need, and provides a suite of capabilities that are valued by the community.”

A vocabulary is not only useful for humans, but also for machines. ARDC-hosted vocabularies follow contemporary best practice whereby each term is allocated a unique web identifier.

The information is structured using the Simple Knowledge Organization System (SKOS), the W3C recommendation for representing vocabularies in a format understandable by computers. This supports interoperability and reuse of the vocabulary term, and discovery and integration of data.

Governance and Reuse of Vocabularies at IMOS

Dr Natalia Atkins is the metadata manager for all IMOS vocabularies used in managing the Australian Ocean Data Network. She creates all the metadata records for IMOS content, using vocabulary terms such as the vessel name and the name of the organisation that collected the data.

“We created our vocabularies to make the IMOS data collections more discoverable. We have separate vocabularies which are used for different workflows. The main use of our vocabularies is for driving the faceted searching on the AODN portal,” said Dr Atkins.

The vocabularies are also used in the data ingestion process [to AODN] to ensure that it is catalogued in a systematic way. “Water temperature is a good example,” said Dr Atkins. “Some people call it ‘temperature of the water body’, others call it ‘sea temperature’; then there’s ‘sea surface temperature’ or ‘SST’. If you don’t mark things up in a systematic way, you can never be sure it’s the same [thing].

“We also try to have good governance and part of that is not reusing terms already used in other vocabularies.”

For example, if a term already exists in a vocabulary of the British Oceanographic Data Centre – whose vocabulary service is the point of truth for many international oceanography initiatives – Dr Atkins will link to it from the IMOS vocabulary. Not only does this avoid duplication, it ensures the definition is always up to date, and the provenance of the definition is visible for all to assess.

Promoting FAIR Research Vocabularies and Fostering Collaboration

Through the power of the semantic web, vocabularies are evolving beyond the simple concept of a dictionary or thesaurus and are beginning to be shared across disciplines and domains.

It’s important that the research community signs up to use vocabularies in their metadata and data. The ARDC plays a leading role in promoting FAIR research vocabularies in Australia and internationally, not just through our Research Vocabularies Australia service but also through our support for the Australian Vocabulary Special Interest Group and through facilitating several working groups.

As the faraway, menacing drip of melting ice grows ever more insistent, dissolving the barriers that prevent researchers from sharing data quickly and easily has never been more necessary.

Reference

  1. “Southern Ocean in-situ temperature trends over 25 years emerge from interannual variability,” Nature Communicationshttps://doi.org/10.1038/s41467-020-20781-1Jump back

Written by Mary O’Callaghan. Reviewed by Jo Savill, Rowan Brownlee, Dr Lesley Wyborn, Rebecca Cowley, Dr Natalia Atkins, Dr Marian Wiltshire, Dr Adrian Burton, Natasha Simons, Adelle Coote, Ian Duncan, Rosie Hicks

Dr Stuart Newman

Therapeutic Innovation Australia

Since completing a PhD in Antarctic Biology from the University of Tasmania, Stuart has built up considerable experience of science policy, pharmaceutical R&D, grant funding, IP management, business development and commercialisation in the university and not-for-profit sectors.|

Stuart joined TIA as CEO in 2017. Under his leadership, TIA has focussed investment on the gap between research and development of high-value therapeutics, including pharmaceuticals, biologics, vaccines and cell & gene therapies. He also devised an innovative infrastructure access voucher scheme. He is a graduate of the Australian Institute of Company Directors

Beryl Morris

Terrestrial Ecosystem Research Network

Merran Smith

Population Health Research Network

Merran is the inaugural Chief Executive of Australia’s Population Health Research Network and chairs the PHRN Participant Council. She is a past Director of the International Population Data Linkage Network (2019-2020) and current member of the Pawsey Supercomputing Centre Board.

Merran has an extensive background in science, health, and economics with strengths in strategic leadership and many years’ experience in Australia’s health and research infrastructure systems.  She is well versed in data management and oversaw the WA Department of Health’s Health Information Centre for more than 10 years. While with the Department, she established data linkage as a core service and served on Australia’s peak national health information committees. 

Prof Michael Dobbie

Phenomics Australia

Prof. Michael Dobbie has worked to establish and operate Phenomics Australia since its foundation in 2007, serving as CEO since 2013. Prior to leading the development and implementation of these national research infrastructures, Michael was a biomedical research with a PhD in Neurochemistry from the University of London and gained over 20 Years’ experience at the bench in field including genetics, vascular biology, cancer angiogenesis, neuroscience, metabolism, developmental biology, malaria and oxidative stress.

Mark Stickells

Pawsey Supercomputing Centre

Mark is a research executive with more than 20 years’ experience working at a senior level in innovative research and business development roles in complex, multi-stakeholder environments. Through national and international programs and joint-ventures, Mark had successfully led initiatives to accelerate the impact of research, development and education programs for Australia’s key energy, mining and agricultural sectors.
He is a former Chief Executive of an LNG research and development alliance of CSIRO, Curtin University and UWA, partnering with Chevron, Woodside and Shell. Prior to his appointment at Pawsey Mark led the innovation and industry engagement portfolio at The University of Western Australia. In addition, Mark is the current Chair of the Board of All Saints’ College and was appointed an adjunct Senior Fellow of the Perth USAsia Centre (an international policy think tank) in 2017.

Craig Humphrey

National Sea Simulator

Craig Humphrey has worked at AIMS for more than 25 years. He presently serves as the Director of the National Sea Simulator, a position he has held for the last two years. During the ten years preceding his directorial role, Craig was instrumental in the initial conceptualisation, creation, and implementation of the SeaSim. Prior to joining the SeaSim team, Craig worked as an experimental scientist at AIMS for 15 years, where he conducted research on various projects including fish ecotoxicology, inshore reef biological indicators of water quality, and coral reef climate-related studies.

Wojtek Goscinski

National Imaging Facility

Prof Wojtek Goscinski, with over two decades of leadership in research and innovation, heads the National Imaging Facility (NIF), Australia’s premier imaging network. As CEO, he oversees NIF’s collaboration among universities, research institutes, and government agencies. An Adjunct Professor at Monash University, he contributes to the Faculty of Medicine, Nursing and Health Sciences. Prof Goscinski’s notable past roles include founding MASSIVE, a high-impact national analytics facility. He also serves on the Scientific Advisory Committee for Euro Bioimaging ERIC and has led significant international neuroinformatics programs.

Prof Sean Smith

National Computational Infrastructure

Sean Smith commenced as Director of the NCI in January 2018 and is conjointly Professor of Computational Nanomaterials Science and Technology at ANU. He has extensive theoretical and computational research experience in chemistry, nanomaterials and nano-bio science and technology.

Dr Lisa Yen

Microscopy Australia

Lisa is currently Microscopy Australia’s Chief Operating Officer and has over 15 years of experience in university administration, strategic research management in Centres of Excellence, and operations and management of national collaborative research infrastructure. She has been with Microscopy Australia since 2019. Lisa has a doctorate in cognitive science and a first–class honours degree in psychology.

Tamin Darwish

National Deuteration Facility (ANSTO)

Tamim leads the National Deuteration Facility at ANSTO, managing its operations and scientific advancements. With a Ph.D. in Chemistry, his expertise spans deuterium labeling, NMR spectroscopy, and organic synthesis. Tamim’s research focuses on creating deuterated molecules for advanced analytical techniques. His career includes postdoctoral fellowships and contributions to the field as a member of prestigious science communities and committees. His dedication to chemistry and material science is evident in his extensive work and achievements in the field.

Michael Steer

Southern Coastal Research Vessel Fleet

Professor Mike Steer is the Research Director at the South Australian Research and Development Institute (SARDI), with over 20 years of expertise in marine science. He specialises in fish biology, fisheries science, cephalopod ecology, and fishery reform. Dr. Steer has led numerous research initiatives that have significantly advanced Australia’s seafood industry. He is known for fostering collaborations between academia and industry to address challenges in aquatic ecosystems. Prof. Steer holds a PhD from the University of Tasmania and serves on several national committees, including the National Coastal Research Vessels Working Group and the National Marine Science Committee.

Toni Moate

Marine National Facility (CSIRO)

Toni Moate is Director of the Marine National Facility and Director of CSIRO’s National Collections and Marine Infrastructure business unit. 

Toni is responsible for ensuring CSIRO’s national collections and marine infrastructure programs and research areas are effectively positioned, managed and utilised for long term financial sustainability and support science delivery in the national interest. 

Toni has extensive experience in strategic, financial, project and stakeholder management and has worked for CSIRO for over 30 years. In 2015 Toni was awarded the Public Service Medal for outstanding public service in Australian marine and atmospheric science, as part of the Queen’s Birthday Honours List. This was followed in 2017 when Toni was awarded the Tasmanian Telstra Business Woman of the Year. 

Dr Michelle Heupel

Integrated Marine Observing System

Michelle Heupel, with over two decades in marine science, leads Australia’s Integrated Marine Observing System (IMOS) at the University of Tasmania. Her work, pivotal in deploying oceanic observing equipment, supports marine and climate research. Heupel’s expertise in marine predator ecology, especially sharks, is recognized globally. She has a BSc in Zoology and a PhD in Marine Science, contributing to over 160 scientific papers. Her roles have included Vice Chair of Strategy for the IUCN Shark Specialist Group and advisor for the Ocean Tracking Network. Heupel’s dedication to marine conservation and management reflects her profound impact on the field.

Thomas McGoram

Heavy Ion Accelerators

James Whisstock

European Molecular Biology Laboratory Australia

Professor James Whisstock is based at Monash University, where he is currently an Australian Research Council Laureate Fellow, an Honorary National Health and Medical Research Council Senior Principal Research Fellow and Deputy Dean Research in the Faculty of Medicine Nursing and Health Sciences.

Ceri Brenner

Centre for Accelerator Science (ANSTO - Nuclear Science Facilities)

Andrew Gilbert

Bioplatforms Australia

Andrew Gilbert has been Bioplatforms Australia’s general manager since its inception in 2007.
He is a graduate of the Australian Institute of Company Directors. Andrew oversees the investment of $300 million in Commonwealth Government research infrastructure funding in the discovery sciences of genomics, proteomics and metabolomics.
Andrew has an extensive network of contacts from Commonwealth and State Governments, along with prominent universities, medical research institutes, agricultural research institutes and commercial entities. The Bioplatforms Australia network now supports 4500 users per annum across the spectrum of pure research to commercial production. In addition to managing the national infrastructure network, Andrew has also catalysed the formation of a series of strategic national scientific collaborations.
Each of these projects is by design multi-disciplinary, multi-institutional and contain both discovery implications and pathways to end use.

Prof Pascal Perez

Aurin

Professor Pascal Perez is a specialist of Integrative Social Simulation, using Multi-Agent Systems technologies to explore complex infrastructure systems. He is a Fellow of the Royal Society of NSW and the Modelling and Simulation Society of Australia and New Zealand (MSSANZ). 

Professor Perez has published 200 refereed articles and book chapters. In 2002, he received an ARC-International Linkage Fellowship to develop social modelling research at the Australian National University. In 2006, he co-edited with his colleague David Batten the book ‘Complex Science for a Complex World’ (ANU E Press).

Rosie Hicks

Australian Research Data Commons

Rosie has 20 years’ experience working in Australia’s research infrastructure sector. With a career spanning every aspect of scientific instrumentation from product development and technical marketing to managing multi-user facilities, she works across academic and industry domains to drive innovation and research translation.

Richard Dichmann

Australian Plant Phonemics Facility

Richard is committed to advancing Australian agriculture through strengthening sustainable industry partnerships and creating new business opportunities which capitalise on innovation. His career with Bayer spans more than 25 years and five countries in roles ranging from marketing, technology scouting and sustainability. Hailing from rural Victoria and educated in Melbourne, Richard obtained an honours degree in Forestry from Melbourne University and a master’s degree in Agriculture, focusing on satellite remote sensing, from the University of Sydney. Richard is a graduate of the Australian Institute of Company Directors. As Head of Public and Government Affairs ANZ for Bayer Australia and New Zealand, Richard is dedicated to increasing awareness and understanding among political stakeholders of the critical role innovation plays in meeting the food supply and health challenges of the future. Richard is a proud ambassador for Australian agriculture and is married with four children.

Dr Jane Fitzpatrick

Australian National Fabrication Facility

Jane led ANFF’s Queensland node for a number of years, joining the HQ team as its Chief Operating officer in 2012, before becoming CEO in 2021. Her responsibilities include ensuring the network performs as a cohesive and collaborative community, and maximising ANFF’s ability to support projects from academia and industry.

Prof Andy Hogg

Australian Earth System Simulator (ACCESS-NRI)

Professor Andy Hogg is a distinguished climate scientist leading the ACCESS-NRI, where he oversees the development of Australia’s advanced climate models. As a key figure in COSIMA, he contributes to ocean-sea ice model research. His role as a Chief Investigator at the ARC Centre of Excellence for Climate Extremes underscores his commitment to understanding climate dynamics and extremes. His work is pivotal in shaping Australia’s approach to climate science and modeling, reflecting his dedication to environmental research and innovation.

Jamie Schultz

Australian Centre for Neutron Scattering (ANSTO - Nuclear Science Facilities)

Dr Debbie Eagles

Australian Centre for Disease Preparedness (CSIRO)

Debbie Eagles is currently the Director of CSIRO’s Australian Centre for Disease Preparedness (ACDP). Prior to this, Debbie’s roles with ACDP included 4 years as ACDP Deputy Director and 3 years as the Research Director for the Diagnosis, Surveillance and Response (DSR) Program.

Debbie is a veterinarian by training and a World Organisation for Animal Health (WOAH) Reference Laboratory Expert on Bluetongue Virus. She is also enrolled as a WOAH and Australian Qualified Expert on the UN Secretary-General Mechanism’s (UNSGM) Roster for investigations of Alleged Use of Chemical, Biological or Toxin Weapons, has postgraduate qualifications in veterinary public health and has a special interest in interactions at the field/laboratory interface. Debbie has extensive experience in working in the Asia Pacific region, including in laboratory capacity building projects, in field investigations and through the provision of training courses.

Heath Marks

Australian Access Federation

Heath Marks was appointed by the Council of Australian University Directors of Information Technology (CAUDIT) in July 2009 to head a team to deliver the sustainable operations of Australia’s Trust and Identity services for Research and Education. This includes the national trust authentication framework the Australian Access Federation (AAF), and the Open Researcher and Contributor ID (ORCID) Consortium Lead for Australia. He is an IT professional with a wealth of management experience in the successful delivery of transformational Information Technology within the tertiary education and research sector supporting the National Collaborative Research Infrastructure Strategy (NCRIS). Heath participates in many national and international committees and working groups on trust, identity, cyber security, and company strategy. 

Tim Rawling

AuScope

Tim Rawling is the CEO of AuScope Limited. AuScope is Australia’s provider of research infrastructure to the national geoscience community working on fundamental geoscience questions and grand challenges — climate change, natural resources security and natural hazards. Prior to this role, he was Director of Infrastructure Development for AuScope’s Australian Geophysical Observing System (AGOS). His recent research has involved the development of regional/crustal-scale 3D and 4D geological models as well as new exploration methodologies involving 3D modelling and finite element simulation. Tim’s background is in structural geology and IT and he has previously worked as a consultant exploration geologist, as the manager of the 3D modelling and simulation programs at GeoScience Victoria (DPI), as the MCA funded lecturer at the University of Melbourne, a commercial programmer and as a researcher at Monash University and the University of Arizona.

Dr Andre Zerger

Atlas of living Australia

Dr. Andre Zerger is the Director of the Atlas of Living Australia (ALA). The ALA is Australia’s national biodiversity database, harmonising the nation’s biodiversity data to support world-class science and decision-making.  The ALA is hosted by CSIRO and supported by the Commonwealth Government’s NCRIS program. Andre’s background is in the spatial sciences, environmental modelling with a focus on the ecological sciences, and spatially explicit hazard risk modelling. His career has focussed on establishing high-performing teams to deliver national data infrastructure transformations that support research, environmental management, and major government policy initiatives. He has previously led similar programs and held academic positions at the Bureau of Meteorology, CSIRO Ecosystems Sciences, The University of Melbourne, and the University of California.

Andre holds a Bachelor of Science with Honours (Geography, Monash University), a Master of Applied Science (Spatial Information Systems, University of Melbourne), and a PhD (Environmental Science, Australian National University). He is a graduate of the Australian Institute of Company Directors.

Mark McAuley

Astronomy Australia

Mark McAuley has worked for thirty years in research and development environments, with responsibility for securing investments, facilitating collaborations, and executing projects. As CEO of Astronomy Australia Limited, he is responsible for the NCRIS astronomy programme. Mark has previously worked for CSIRO, and in private industry, including six years in computer-aided engineering. His experience ranges from explaining science to young children to leading financial strategy discussions concerning billion-dollar research infrastructure projects.

Mark holds a Master of Business Administration, Master of Arts (Ancient History), and Bachelor of Science with Honours (Astrophysics). Upon completion of his MBA, he received the Vice-Chancellor’s Medal from the University of Notre Dame, Australia.