Developing a one health data integration framework focused on real-time pathogen surveillance and applied genomic epidemiology
Bibliographic record
Abstract
BACKGROUND: The One Health approach aims to balance and optimize the health of humans, animals, and ecosystems, recognizing that shared health outcomes are interdependent. A One Health approach to disease surveillance, control, and prevention requires infrastructure for coordinating, collecting, integrating, and analyzing data across sectors, incorporating human, animal, and environmental surveillance data, as well as pathogen genomic data. However, unlike data interoperability problems faced within a single organization or sector, data coordination and integration across One Health sectors requires engagement among partners to develop shared goals and capacity at the response level. Successful examples are rare; as such, we sought to develop a framework for local One Health practitioners to utilize in support of such efforts. METHODS: We conducted a systematic scientific and gray literature review to inform development of a One Health data integration framework. We discussed a draft framework with 17 One Health and informatics experts during semi-structured interviews. Approaches to genomic data integration were identified. RESULTS: In total, 57 records were included in the final study, representing 13 pre-defined frameworks for health systems, One Health, or data integration. These frameworks, included articles, and expert feedback were incorporated into a novel framework for One Health data integration. Two scenarios for genomic data integration were identified in the literature and outlined. CONCLUSIONS: Frameworks currently exist for One Health data integration and separately for general informatics processes; however, their integration and application to real-time disease surveillance raises unique considerations. The framework developed herein considers common challenges of limited resource settings, including lack of informatics support during planning, and the need to move beyond scoping and planning to system development, production, and joint analyses. Several important considerations separate this One Health framework from more generalized informatics frameworks; these include complex partner identification, requirements for engagement and co-development of system scope, complex data governance, and a requirement for joint data analysis, reporting, and interpretation across sectors for success. This framework will support operationalization of data integration at the response level, providing early warning for impending One Health events, promoting identification of novel hypotheses and insights, and allowing for integrated One Health solutions.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.120 | 0.085 |
| Meta-epidemiology (narrow) | 0.002 | 0.002 |
| Meta-epidemiology (broad) | 0.002 | 0.005 |
| Bibliometrics | 0.024 | 0.015 |
| Science and technology studies | 0.006 | 0.010 |
| Scholarly communication | 0.014 | 0.022 |
| Open science | 0.007 | 0.014 |
| Research integrity | 0.006 | 0.006 |
| Insufficient payload (model declined to judge) | 0.003 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".