– ABOUT
AUSTRALIAN ANIMAL DISEASE GENOMICS INITIATIVE

OBJECTIVES
In collaboration with the animal health community, this initiative enhances disease research and biosecurity through two key efforts:
1) Reference Genome Library – Sequencing and annotating high-quality genomes of priority animal pathogens, including bacteria, fungi, viruses, and parasites. These resources will be openly available to support disease understanding and management.
2) Animal Virome Atlas – Metagenomic sequencing to map virus diversity in animals, exploring how virome structures change and assessing ecological and evolutionary disease drivers.
By generating open-access genomic data, this initiative strengthens Australia’s ability to understand, monitor, manage, and respond to animal disease threats.
PROJECTS
| Scientific name | Project Summary | Data Strategy | Project Lead | Partners | |
|---|---|---|---|---|---|
| Theme 1: Reference Genome Library | Coxiella burnetii (Q fever) | Generate complete genome sequences for C. burnetii isolates to improve understanding of strain diversity and transmission pathways in humans and livestock. The data will enhance detection methods and strengthen surveillance and research into vaccine and disease control strategies. | Reference genome (PacBio HiFi) | Tarka Raj Bhatta | Barwon Health, Australian Rickettsial Reference Laboratory; Deakin University; The University of Melbourne; Monash University |
| Theme 1: Reference Genome Library | Moraxella spp. | Produce genomic data on Moraxella strains associated with pinkeye in cattle. The project will assess antimicrobial resistance and strain variation to improve diagnostic precision and inform management practices in the livestock sector. | Reference genome (ONT) | Barbara Brito | NSW Department of Primary Industries and Regional Development; University of Technology Sydney; The University of Sydney |
| Theme 1: Reference Genome Library | Vibrio spp. | Create genomic references for Vibrio species affecting farmed aquatic animals. The data will support improved diagnostics, monitoring of disease spread, and management decisions to protect aquaculture productivity. | Reference genome (ONT) | Mei Ooi | Department of Natural Resources and Environment Tasmania - Animal Health Laboratory |
| Theme 1: Reference Genome Library | Trypanosoma spp. | Generate genomic assemblies of newly discovered trypanosome species. The project will clarify parasite life cycles, improve understanding of transmission pathways, and identify biological vulnerabilities that can inform treatment and management strategies for wildlife, livestock, and potential human infections. | Reference genome (PacBio HiFi, Illumina), Transcriptomics (Illumina) | Alexander Maier | The Australian National University |
| Theme 1: Reference Genome Library | Teladorsagia circumcincta (Brown stomach worm) | Develop a reference genome for T. circumcincta to investigate population structure and resistance mechanisms. The data will advance diagnostic capability, support vaccine development, and underpin improved parasite control in Australian sheep industries. | Reference genome (PacBio HiFi, Hi-C) | Annaleise Wilson | CSIRO |
| Theme 1: Reference Genome Library | Marteilia sydneyi (QX disease) | Generate genomic resources for M. sydneyi, the causative agent of QX disease in oysters. The genome data will enhance diagnostic tools, inform selective breeding for resistance, and strengthen management of aquaculture biosecurity risks. | Reference genome (PacBio HiFi, ONT, Hi-C), Transcriptomics (Iso-seq) | Ido Bar | Griffith University; NSW Department of Primary Industries and Regional Development; QLD Department of Agriculture and Fisheries; University of St Andrews (Scotland) |
| Theme 2: Animal Virome Atlas | Honeybee virome (Apis mellifera & Varroa destructor | Tracks changes in the viral landscape of honey bees (Apis mellifera) tracking how the honey bee virome shifts before, during, and after Varroa invasion in specific NSW regions. Focuses on novel virus discovery, diagnostic development, and understanding Varroa-vectored viral emergence. | Virome sequencing (short read) | Emily Remnant | The University of Sydney |
| Theme 2: Animal Virome Atlas | Native stingless bee virome (Tetragonula carbonaria) | Surveys viral diversity in wild and managed colonies of Tetragonula carbonaria across Queensland and New South Wales. Compares viromes between wild, managed, and co-located hives with honey bees to assess viral spillover risk and inform pollinator biosecurity and management. | Virome sequencing (short read) | Emily Remnant | The University of Sydney; Macquarie University |
| Theme 2: Animal Virome Atlas | Tick virome (Ixodes spp.) | Profiles viruses from five Sternalixodes tick species collected in Queensland and northern New South Wales using museum and field samples. Identifies shared and unique viral signatures to improve understanding of tick-borne virus ecology and zoonotic disease potential. | Virome sequencing (short read) | Rhys Parry | The University of Queensland |
| Theme 2: Animal Virome Atlas | Dragon lizard virome (Agamidae spp.) | Characterises viruses in wild and captive dragon lizards from multiple regions. Compares healthy and diseased animals, including threatened species, to identify novel viruses and inform reptile disease monitoring and conservation management. | Virome sequencing (short read) | Julien Melade | The University of Sydney; University of Canberra |
| Theme 2: Animal Virome Atlas | Koala virome (Phascolarctos cinereus) | Characterises the respiratory virome of koalas by integrating viral, bacterial, fungal, and host immune data to identify drivers of disease susceptibility and potential biomarkers of infection risk. Outputs include novel RNA virus discovery, ecological and evolutionary analysis of viral communities, and insights into microbiome–virome–immunity interactions that inform wildlife health and conservation strategies. | Virome sequencing (short read) | Kosuke Takada | The University of Sydney |
| Theme 2: Animal Virome Atlas | Marsupials virome (multiple species) | Uses archived diagnostic samples from Victorian marsupials (including wombats, koalas, kangaroos, and wallabies) to detect known and novel viruses. Links viral presence to disease presentation, improving diagnostic capability and clinical management for wildlife health programs. | Virome sequencing (short read) | Alistair Legione | The University of Melbourne (Asia-Pacific Centre for Animal Health) |
| Theme 2: Animal Virome Atlas | Endangered marsupial virome | Examines viruses in two endangered marsupials (Lasiorhinus krefftii and Perameles bougainville) from Western Australia and Queensland to identify novel viral species and assess ecological and evolutionary patterns. Data will inform conservation strategies, early disease detection, and translocation management. | Virome sequencing (short read) | Ayda Susana Ortiz Baez | The University of Sydney |
| Theme 2: Animal Virome Atlas | Wildlife–Domestic interface virome | Explores virome diversity across domestic and wild species (including kangaroos, ducks, and dogs) to identify viral families shared among taxa and better understand potential cross-species transmission pathways. | Virome sequencing (short read) | Subir Sarker | James Cook University |
| Theme 2: Animal Virome Atlas | Queensland Wildlife Virome (multiple species) | Samples a wide range of native mammals (e.g. kangaroos, possums, quolls) and birds admitted to the Australia Zoo Wildlife Hospital in Queensland to characterise both known and novel viruses. The project generates high-quality virome datasets to assess host–virus dynamics, zoonotic potential, and viral diversity, strengthening wildlife disease surveillance and One Health biosecurity outcomes. | Virome sequencing (short read) | Subir Sarker | James Cook University; University of the Sunshine Coast |
| Theme 1: Reference Genome Library | Actinobacillus pleuropneumoniae | Actinobacillus pleuropneumoniae (App) causes major economic losses in Australian pig production. This project will generate genomic data from well‑characterised Australian App isolates with clinical metadata to identify strain diversity, virulence and biofilm factors, supporting improved surveillance, targeted control, and vaccine development. | Reference genome (PacBio HiFi) | Lida Omaleki | University of Queensland, Queensland Alliance for Agriculture and Food Innovation |
| Theme 1: Reference Genome Library | Avibacterium paragallinarum | This project will use RNA sequencing to identify the genes involved in helping the chicken pathogen Avibacterium paragallinarum grow in the lab, and why the Australian strains can grow despite key gene loss. We expect to use the outcomes of this project to inform industry partners on improved methods for growing A. paragallinarum, and to improve treatment of Australian strains. | Whole Genome Sequencing, Transcriptomics (Illumina) | Sean Bisset | University of Queensland, QAAFI |
| Theme 1: Reference Genome Library | Klebsiella pneumoniae | Klebsiella pneumoniae (KP) is a bacterium that causes live-threatening infections in people and dairy cows and is sometimes found in healthy chickens. KP can jump between host species and it “traffics” drug resistance genes. We want to understand which types of KP occur in Australian livestock, how they compare to human KP, and how we can prevent or treat infections with KP in people and animals. | Reference genome (PacBio HiFi), Whole Genome Sequencing | Ruth Zadoks | University of Sydney |
| Theme 1: Reference Genome Library | Mycobacterium ulcerans | This project will generate genomic data for Mycobacterium ulcerans, the cause of Buruli ulcer, using possum samples to investigate its spread in emerging areas of Geelong. By comparing strains across locations, it will determine whether infections arise from local transmission or independent introductions, informing surveillance, risk mapping, and One Health responses. | Whole Genome Sequencing | Alyssa Barry | Deakin University, CSIRO –The Australian Centre for Disease Preparedness (ACDP) |
| Theme 1: Reference Genome Library | Pasteurella multocida | This project will generate high quality genomic data from Australian Pasteurella multocida isolates associated with severe respiratory disease in pigs. By linking genomics with clinical and diagnostic data, the project aims to improve understanding of strain diversity and support enhanced surveillance, diagnostics, and disease control for the Australian pig industry. | Reference genome (ONT) | Lida Omaleki | University of Queensland, Queensland Alliance for Agriculture and Food Innovation, NSW DPIRD |
| Theme 1: Reference Genome Library | Cryptococcus gattii species complex | Focusing on the relationship between environmental and koala C. gattii isolates, this study aims to create genomic data for koala and environmental C. gattii isolates and verify their correlation with the stage of host-pathogen interaction. We expect to fill gaps in current genomic data related to C. gattii and detect genetic variations contributing to host adaptation and infection outcomes. | Whole Genome Sequencing | Luisa Miranda | University of Sydney, Westerdijk Fungal Biodiversity Institute |
| Theme 1: Reference Genome Library | Nannizziopsis sp. | This project aims to generate high-quality reference genomes for Nannizziopsis species, addressing the critical lack of fully annotated genomic data. The resulting data will be deposited in the public domain, providing a valuable resource for future research and application and mitigating the impact of YFD on reptile health and biodiversity. | Reference genome (PacBio HiFi, Hi-C), Transcriptomics (Illumina) | Mariana Williams | Queensland Department of Primary Industries |
| Theme 1: Reference Genome Library | Brachylaima cribbi | This project will provide the first reference genome for Brachylaima cribbi, a zoonotic parasite causing gastrointestinal disease in humans and wildlife in Australia. This will be the first genome for the family Brachylaimidae. The data will permit identification of the parasite to move beyond morphology, facilitating development of molecular and veterinary diagnostics. | Reference genome (PacBio HiFi, Hi-C), Transcriptomics (Illumina) | Dan Huston | CSIRO, University of Canberra |
| Theme 1: Reference Genome Library | Cryptosporidium parvum | Cryptosporidium parvum in an important parasite of animals and humans in Australia and globally causing mild to severe diarrhea which can lead to death. There are currently no Australian reference genomes for this species. Reference genomes from a pig hosy of Australian Cryptosporidium parvum will be generated to enable genomic surveillance in Australia. | Reference genome (ONT, Hi-C), Transcriptomics (Illumina) | Marielle Babineau | University of Melbourne - Centre for Pathogen Genomics, School of Veterinary Science, Microbiological Diagnostic Unit Public Health Laboratory |
| Theme 1: Reference Genome Library | Nematodirus filicollis | Generate first reference genome for Nematodirus filicollis, a major Australian sheep/goat parasite. Outcomes: Molecular identification tools, anthelmintic resistance markers, epidemiological insights for improved livestock health management across Australia's temperate grazing regions. | Reference genome (PacBio HiFi, Hi-C), Transcriptomics (Illumina) | Erwin Pazmunoz | The University of Western Australia, Department of Primary Industry WA, |
| Theme 1: Reference Genome Library | Strongyloides stercoralis | This project applies a genomics-driven One Health approach to strongyloidiasis in Indigenous communities. It will analyse S. stercoralis genomes from dogs and humans to identify transmission pathways, genetic markers, and drivers of severe disease, supporting development of sensitive diagnostics, improved surveillance, more targeted control strategies, and ultimately reduced disease burden. | Reference genome (PacBio HiFi, Hi-C), Transcriptomics (Illumina), Whole Genome Sequencing | Patsy A. Zendejas Heredia | The University of Melbourne |
| Theme 1: Reference Genome Library | Cryptocaryon irritans | Cryptocaryon irritans causes disease in marine fish aquaculture. A lack of knowledge in the parasite genome limits diagnostics and genetic approaches towards management. This project will deliver genomic information that will be applied to establish sensitive diagnostics to monitor the parasite in the environment and direct vaccination and genetic approaches to prevent disease. | Reference genome (ONT, Hi-C), Transcriptomics (Illumina) | Kelly Condon | James Cook University, Mainstream Aquaculture |
| Theme 1: Reference Genome Library | Eimeria echidnae | Echidnas are highly susceptible to a protozoan parasite that can cause death in hours. The echidna parasite infect many different body systems compared to other animal hosts where it is confirmed to the gut. Eimeria in echidna are also ancient parasites and over 100 million years old. These data will inform echidna health, and also provide wider knowledge for other important parasites. | Reference genome (ONT, Hi-C), Transcriptomics (Illumina) | Michelle Power | Macquarie University, Taronga Wildlife Hospital |
| Theme 1: Reference Genome Library | Neospora caninum | This project is investigating the discovery of a new protozoan parasite that impacts farm and domestic animals in the endangered Australian sea lion. We aim to determine if sea lions have acquired this parasite from land animals or if they have their own species. Sea lions are already susceptible to the hookworm parasite and these data will help manage sea lion health. | Reference genome (ONT, Hi-C), Transcriptomics (Illumina) | Michelle Power | Macquarie University, University of Sydney |
| Theme 1: Reference Genome Library | Arboviruses (focusing on orthobunyaviruses, orthoflaviviruses and alphaviruses) | The Doherty Collection contains a comprehensive archive of arboviruses. However, the collection remains largely uncharacterised with limited genomic/provenance data. Sequencing this collection will generate critical genomic data that will advance our understanding of animal pathogens and support phylogenetic classification/resolution of viral lineages, through comparison with contemporary isolates | Transcriptomics (Illumina) | Wilson Nguyen | QIMR Berghofer |
| Theme 1: Reference Genome Library | Oyster herpesvirus OsHV-1 | This project will sequence the virus responsible for major oyster deaths in Australia. By analysing a unique collection of samples, we will track how the virus spreads, changes over time, and causes disease. The results will help protect the oyster industry, improve biosecurity responses, and support development of new solutions such as vaccines. | Whole Genome Sequencing | Francisca Samsing | University of Sydney, LABÉO (Université de Caen Normandie, France), NSW DPIRD |
| Theme 1: Reference Genome Library | Haemaphysalis humerosa | This project will generate a high-quality reference genome for the Australian tick Haemaphysalis humerosa and associated metagenomic data to characterise bacterial and viral diversity. It aims to improve understanding of tick-associated pathogens, their potential role in wildlife disease cycles, and support molecular surveillance and biosecurity monitoring in Australia. | Reference genome (PacBio HiFi, Hi-C), Transcriptomics (Illumina) | Swaid Abdullah | University of Queensland |
| Theme 2: Animal Virome Atlas | Whale Sharks (Rhincodon typus) | We will characterise the virome of whale sharks at Ningaloo Reef across multiple years to assess the impact of a climate-driven heatwave. We will identify viral diversity, function, and the relationship with the microbiome and links to host health. Outcomes will provide the first virome baseline for any shark species and inform conservation and environmental monitoring. | Virome sequencing (short read) | Elizabeth Dinsdale | Flinders University, University of Western Australia |
| Theme 2: Animal Virome Atlas | Koala (Phascolarctos cinereus) | The virome of South Australian koalas across populations with differing genetic diversity and disease status. Using existing faecal samples and genomic data, iidentifying novel viruses and linking viral diversity to koala health. Outcomes will improve modelling of disease dynamics, support conservation, and guide management decisions such as translocation to enhance population resilience. | Virome sequencing (short read) | Elizabeth Dinsdale | Flinders University |
| Theme 2: Animal Virome Atlas | Wild pig (Sus scrofa) | This project will characterise the virome of feral pigs in Far North Queensland's Northern Peninsula Area using metagenomic sequencing of swab samples. By linking viral diversity data with camera-trap records of scavenger activity, we will assess spillover risk to dingoes, domestic dogs, and humans stemming from carcasses, also generating the first comprehensive virome atlas for this region. | Virome sequencing (short read) | Jessica Agius | University of Sydney, Centre for Infectious Diseases and Microbiology - Public Health (CIDM-PH), Westmead Hospital, Elizabeth Macarthur Agricultural Institute (EMAI, NSW DPIRD) |
| Theme 2: Animal Virome Atlas | 13 co-occurring seabird species from the Norfolk Island–Phillip Island system: Little Shearwater (Puffinus assimilis), Providence Petrel (Pterodroma solandri), Wedge-tailed Shearwater (Ardenna pacifica), Grey Ternlet (Anous albivitta), Common Noddy (Anous stolidus), Masked Booby (Sula dactylatra), Flesh-footed Shearwater (Ardenna carneipes), White-necked Petrel (Pterodroma cervicalis), Kermadec Petrel (Pterodroma neglecta), Red-tailed Tropicbird (Phaethon rubricauda), Sooty Tern (Onychoprion fuscatus), Black-winged Petrel (Pterodroma nigripennis), and Black Noddy (Anous minutus). | This project will generate a multi-species virome atlas for Norfolk Island seabirds using metagenomic sequencing. The dataset will reveal viral diversity across a key South-West Pacific island seabird community, identify viruses of conservation or biosecurity relevance, and guide future wildlife disease surveillance. | Virome sequencing (short read) | Jane Younger | University of Tasmania |
| Theme 2: Animal Virome Atlas | Snowy sheathbill (Chionis albus), southern giant petrel (Macronectes giganteus), and brown skua / Antarctic skua complex (Stercorarius antarcticus / Stercorarius lonnbergi), gentoo penguin (Pygoscelis papua), king penguin (Aptenodytes patagonicus), macaroni penguin (Eudyptes chrysolophus) | This project will generate the first virome atlas for sub-Antarctic seabirds from Heard Island and South Georgia. By sequencing six shared species across both islands, including rare Heard Island samples, it will identify viral diversity, novel viruses and patterns of viral sharing to guide future disease surveillance on Australia’s sub-Antarctic islands. | Virome sequencing (short read) | Jane Younger | University of Tasmania, Australian Antarctic Division (AAD), Cornell University, Universite de Montpellier |
| Theme 2: Animal Virome Atlas | Gentoo Penguins (Pygoscelis papua) | This project will reveal viromes of Gentoo Penguins. We will clarify viral diversity and reveal the extent of viral incursions and connectivity across an Antarctic penguin metapopulation. These data will support risk assessments, development of a coordinated evidence-based surveillance framework, and disease management in region rapidly changing due to anthropogenic and climate change. | Virome sequencing (short read) | Michelle Wille | University of Melbourne, Federation University |
| Theme 2: Animal Virome Atlas | Magpie Goose (Anseranas semipalmata), Plumed Whistling Duck (Dendrocygna eytoni), Radjah Shelduck (Radjah radjah) | This project will generate virome profiles of wild birds in northern Australia to characterise known and novel viruses. The data will improve our understanding of the role of wild birds as reservoirs for novel viruses which may pose a risk to Australia, potential cross-species transmission pathways, inform disease surveillance priorities and strengthen preparedness for future disease threats | Virome sequencing (short read) | Michelle Wille | University of Melbourne, Northern Land Council, Deakin University, Western Australia Department of Health |
| Theme 2: Animal Virome Atlas | Abalone, Haliotis laevigata, Haliotis rubra | This project will generate the first comprehensive virome atlas of abalone, identifying known and novel viruses across farmed and wild populations. The aim is to establish a baseline for viral diversity to support disease surveillance, early detection of emerging pathogens, and improved biosecurity and management of abalone industries. | Virome sequencing (short read) | Travis Beddoe | La Trobe University |
| Theme 2: Animal Virome Atlas | Cherax quadricarinatus | This project will characterise the virome of wild redclaw crayfish from two northern Queensland freshwater systems. It aims to identify known and novel viruses and compare virome composition between populations. Outcomes will support disease surveillance, biosecurity risk assessment for aquaculture, and future virus discovery and research. | Virome sequencing (short read) | Jennifer Elliman | James Cook University |
| Theme 2: Animal Virome Atlas | Sea stars, sea urchins, sea cucumbers (Echinoderms) | The focus of this project is to characterise the under-explored virus diversity of echinoderms in Australia using metatranscriptomics. The aims are to answer key questions behind RNA virus evolution, virus community structure, and disease biology to aid in the development of population management and conservation strategies. | Virome sequencing (short read) | Kate Van Brussel | University of Sydney |
| Theme 2: Animal Virome Atlas | Scleractinian corals | Corals are keystone animals that are threatened by rising ocean temperatures and disease. This project will characterise the viromes of healthy, stressed, and diseased corals in Western Australia and overseas territories. Focusing on systems beyond the Great Barrier Reef, this project addresses a major knowledge gap and will underpin effective ecological surveillance of western coral ecosystems. | Virome sequencing (short read) | Mary Petrone | University of Sydney, Curtin University |
| Theme 2: Animal Virome Atlas | Ascidians (subplyhum: Tunicata) | This project explores the hidden world of viruses associated with ascidians in temperate Australian waters. By sequencing RNA from colonial and solitary species collected in NSW and WA, it aims to discover new viruses and investigate their potential as pathogens. | Virome sequencing (short read) | Miguel Perea | University of Sydney |
| Theme 2: Animal Virome Atlas | Amegilla cingulata (blue-banded bees) and Eristalis tenax (hoverflies) | This project will unlock the hidden viral communities of native Australian pollinators by comparing wild and domesticated blue-banded bees and hoverflies. It will reveal viral diversity and transmission patterns, helping to improve pollinator health, strengthen disease surveillance, and support the sustainable development of domesticated pollination systems. | Virome sequencing (short read) | Sabrina Haque | University of Sydney, Macquarie University |
| Theme 2: Animal Virome Atlas | Microbat | Despite the global impact of viruses, we know little about those circulating in Australian wildlife. This project will characterise viromes of microbats in regional NSW to identify zoonotic risks and improve surveillance. Outcomes include a regional virome atlas, enhanced early warning, and data supporting One Health initiatives. | Virome sequencing (short read) | Verlaine Timms | University of Newcastle, Diagnostic Technology, NSW Health Pathology |
PARTNERS
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advisory committee members
| Mark Hutchinson (Chair) | University of Adelaide and SABRE Alliance |
| Edward Holmes | University of Sydney |
| Michelle Wille | University of Melbourne |
| Jess Morgan | QLD Department of Agriculture and Fisheries |
| God’spower Okoh | NT DITT – Berrimah Veterinary Laboratory |
| Guy Weerasinghe | DAFF |
| Stacey Lynch | Australian Centre for Disease Preparedness |
| Sarah Richmond | Bioplatforms Australia |
KEY INFORMATION
ACKNOWLEDGEMENT INFORMATION
Bioplatforms Initiative DOI: https://doi.org/10.25953/qzxv-md52
Umbrella Bioproject ID: PRJNA1217493
Please use this ID when submitting any derived data to a database that is a member of the International Nucleotide Sequence Database Collaboration (INSDC), such as GenBank/NCBI, ENA or DDBJ.
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Citation Guidelines
To cite the general initiative:
Australian Animal Disease Genomics Initiative, 2025, https://doi.org/10.25953/qzxv-md52
To cite a specific dataset:
The Australian Animal Disease Genomics Initiative, 2025, https://doi.org/10.25953/qzxv-md52, [year-of-data-download], [full dataset title], [dataset-access-URL], accessed [date-of-access].
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Acknowledgement Statement
We would like to acknowledge the contribution of the Australian Animal Disease Genomics Initiative Consortium in the generation of data used in this publication. The Initiative is supported by funding from Bioplatforms Australia, enabled by the Commonwealth Government National Collaborative Research Infrastructure Strategy (NCRIS).
If relevant, also credit other organisations involved in the collection of the particular dataset you are using, as listed in the ‘project_lead’ and ‘project_collaborators’ in the metadata record.
CONTACT US
Project Manager
Mabel Lum – Bioplatforms Australia
mlum@bioplatforms.com
General Manager
Sarah Richmond – Bioplatforms Australia
srichmond@bioplatforms.com
DATA AND COLLABORATION POLICY
Data generated through this initiative is subject to the Data and Collaboration policy. Please review it here.