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Online Mendelian Inheritance in Animals (OMIA) is a freely available curated knowledgebase that contains information and facilitates research on inherited traits and diseases in animals. For the past 29 years, OMIA has been used by animal geneticists, breeders, and veterinarians worldwide as a definitive source of information. Recent increases in curation capacity and funding for software engineering support have resulted in software upgrades and commencement of several initiatives, which include the enhancement of variant information and links to human data resources, and the introduction of ontology-based breed information and categories. We provide an overview of current information and recent enhancements to OMIA and discuss how we are expanding the integration of OMIA into other resources and databases via the use of ontologies and the adaptation of tools used in human genetics.
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Online Mendelian Inheritance in Animals (OMIA is a freely available information resource, which includes information for Equus inherited traits/diseases (collectively called phenes). The database focuses on Mendelian traits and their likely causal variants (mutations). Some of these Mendelian traits are favored by humans, e.g., coat color, while others are diseases. Additions to OMIA are based on publications of peer-reviewed research. Maintaining up-to-date information in OMIA is a challenge, owing to the multiplicity of species, the increase in the number of relevant publications, and as reference genomes and methods of citation continue to evolve. This challenge has been successfully aided by contributions from scientists from around the world. In some cases, those scientists are faculty members who charge their students with curation as an educational activity. Recently, OMIA has introduced computerized lists of standardized names and synonyms (called ontologies) for breeds of Equus and other animals and for phene categories. These ontologies facilitate increased connectivity between OMIA and other online resources. OMIA is and will continue to be a major reference resource for Mendelian phenes in the genus Equus.
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Background : Limited universally adopted data standards in veterinary science hinders data interoperability and therefore integration and comparison; this ultimately impedes application of existing information-based tools to support advancement in veterinary diagnostics, treatments, and precision medicine. Hypothesis/Objectives : Creation of a Vertebrate Breed Ontology (VBO) as a single, coherent logic-based standard for documenting breed names in animal health, production and research-related records will improve data use capabilities in veterinary and comparative medicine. Animals : No live animals were used in this study. Methods : A list of breed names and related information was compiled from relevant sources, organizations, communities, and experts using manual and computational approaches to create VBO. Each breed is represented by a VBO term that includes all provenance and the breed's related information as metadata. VBO terms are classified using description logic to allow computational applications and Artificial Intelligence-readiness. Results : VBO is an open, community-driven ontology representing over 19,000 livestock and companion animal breeds covering 41 species. Breeds are classified based on community and expert conventions (e.g., horse breed, cattle breed). This classification is supported by relations to the breeds' genus and species indicated by NCBI Taxonomy terms. Relationships between VBO terms, e.g. relating breeds to their foundation stock, provide additional context to support advanced data analytics. VBO term metadata includes common names and synonyms, breed identifiers/codes, and attributed cross-references to other databases. Conclusion and clinical importance : Veterinary data interoperability and computability can be enhanced by the adoption of VBO as a source of standard breed names in databases and veterinary electronic health records.
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BACKGROUND: The CSC study found that the universal delivery of a school-based, online programme for the prevention of mental health and substance use disorders among adolescents resulted in improvements in mental health and substance use outcomes at 30-month follow-up. We aimed to compare the long-term effects of four interventions-Climate Schools Combined (CSC) mental health and substance use, Climate Schools Substance Use (CSSU) alone, Climate Schools Mental Health (CSMH) alone, and standard health education-on mental health and substance use outcomes among adolescents at 72-month follow-up into early adulthood. METHODS: This long-term study followed up adolescents from a multicentre, cluster-randomised trial conducted across three states in Australia (New South Wales, Queensland, and Western Australia) enrolled between Sept 1, 2013, and Feb 28, 2014, for up to 72 months after baseline assessment. Adolescents (aged 18-20 years) from the original CSC study who accepted contact at 30-month follow-up and provided informed consent at 60-month follow-up were eligible. The interventions were delivered in school classrooms through an online delivery format and used a mixture of peer cartoon storyboards and classroom activities that were focused on alcohol, cannabis, anxiety, and depression. Participants took part in two web-based assessments at 60-month and 72-month follow-up. Primary outcomes were alcohol use, cannabis use, anxiety, and depression, measured by self-reported surveys and analysed by intention to treat (ie, in all students who were eligible at baseline). This trial is registered with the Australian New Zealand Clinical Trials Registry (ACTRN12613000723785), including the extended follow-up study. FINDINGS: Of 6386 students enrolled from 71 schools, 1556 (24·4%) were randomly assigned to education as usual, 1739 (27·2%) to CSSU, 1594 (25·0%) to CSMH, and 1497 (23·4%) to CSC. 311 (22·2%) of 1401 participants in the control group, 394 (26·4%) of 1495 in the CSSU group, 477 (37·%) of 1289 in the CSMH group, and 400 (32·5%) of 1232 in the CSC group completed follow-up at 72 months. Adolescents in the CSC group reported slower year-by-year increases in weekly alcohol use (odds ratio 0·78 [95% CI 0·66-0·92]; p=0·0028) and heavy episodic drinking (0·69 [0·58-0·81]; p<0·0001) than did the control group. However, significant baseline differences between groups for drinking outcomes, and no difference in the predicted probability of weekly or heavy episodic drinking between groups were observed at 72 months. Sensitivity analyses increased uncertainty around estimates. No significant long-term differences were observed in relation to alcohol use disorder, cannabis use, cannabis use disorder, anxiety, or depression. No adverse events were reported during the trial. INTERPRETATION: We found some evidence that a universal online programme for the prevention of anxiety, depression, and substance use delivered in early adolescence is effective in reducing the use and harmful use of alcohol into early adulthood. However, confidence in these findings is reduced due to baseline differences, and we did not see a difference in the predicted probability of drinking between groups at 72-month follow-up. These findings suggest that a universal prevention programme in adolescence is not sufficient to have lasting effects on mental health and substance use disorders in the long term. In addition to baseline differences, substantial attrition warrants caution in interpretation and the latter factor highlights the need for future long-term follow-up studies to invest in strategies to increase engagement. FUNDING: Australian National Health and Medical Research Council.