The Infectious Disease Ontology in the Age of COVID-19

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research

Opening up ‘fever’, closing down medicines

Rising concerns about antimicrobial resistance have sparked a renewed push to rationalise and ration the use of medicines. This article explores the case of the Integrated Management of Childhood Illness (IMCI) guideline, a periodically updated ‘global’ algorithm that shapes and normalises the centrality of medicines to care in low- and middle-income countries and, increasingly, the imperative to ration them. Using ‘classification work’ as analytic frame, we firstly consider the IMCI algorithm as a blueprint for global health that classifies illnesses, patients, and care in particular ways relative to available medicines. Zooming in on this blueprint, we then offer a classificatory reading of ‘fever’ over time, tracing ‘nonmalarial fever’ from being malaria’s residual ‘other’ category to becoming increasingly legible through attention to diagnostics and antibiotic (over)use. Our reading suggests that an apparent refinement of the ‘fever’ category may concurrently entail the closing down of medicine options. This raises the possibility that an increasingly high-tech but ‘empty’ form of pharmaceuticalised care is being incidentally worked into the infrastructure of weak health systems

Local interpretations on malaria and the discourse on the traditional health care providers in southern Mozambique

The narratives on the diagnosis and causes of malaria are diverse and apparently ambiguous, being based beyond the body, on the social relations among peers, their ancestors, and nature. Based on a qualitative study and a four-year stay in Mozambique, this article analyzes the discourses of patients and biomedical practitioners on traditional health care providers, i.e., tinyanga and zion pastors, linking them to local terminology of malaria, in a rural district in southern Mozambique. In the current context of therapeutic pluralism and high mobility, the lack of solidarity and compassion attributed to tinyanga is supported by the monetization and commodification of their medicinal rituals and knowledge, as well as by competition with other providers in attracting patients. The implementation of zion churches, of Christian nature and performing therapeutic practices similar to tinyanga, is presented as a local advantageous solution due to the strong community connection, the comfort and reciprocity among the members, and the therapeutic results at low cost. In terms of health care policies and clinical practice, the invisibility of zion pastors and the subordinate role of healers is managed according to interests, based on vague ideas and prejudices from biomedical providers. The implementation of health policies that address the local diversity, the existing power relations and medical knowledge and practices can strengthen the biomedical care services and harmonize relations between the providers and the population.info:eu-repo/semantics/publishedVersio

Multi-Disease Data Management System Platform for Vector-Borne Diseases

Background Emerging information technologies present new opportunities to reduce the burden of malaria, dengue and other infectious diseases. For example, use of a data management system software package can help disease control programs to better manage and analyze their data, and thus enhances their ability to carry out continuous surveillance, monitor interventions and evaluate control program performance. Methods and Findings We describe a novel multi-disease data management system platform (hereinafter referred to as the system) with current capacity for dengue and malaria that supports data entry, storage and query. It also allows for production of maps and both standardized and customized reports. The system is comprised exclusively of software components that can be distributed without the user incurring licensing costs. It was designed to maximize the ability of the user to adapt the system to local conditions without involvement of software developers. Key points of system adaptability include 1) customizable functionality content by disease, 2) configurable roles and permissions, 3) customizable user interfaces and display labels and 4) configurable information trees including a geographical entity tree and a term tree. The system includes significant portions of functionality that is entirely or in large part re-used across diseases, which provides an economy of scope as new diseases downstream are added to the system at decreased cost. Conclusions We have developed a system with great potential for aiding disease control programs in their task to reduce the burden of dengue and malaria, including the implementation of integrated vector management programs. Next steps include evaluations of operational implementations of the current system with capacity for dengue and malaria, and the inclusion in the system platform of other important vector-borne diseases

Local interpretations on malaria and the discourse on the traditional health care providers in southern Mozambique

The narratives on the diagnosis and causes of malaria are diverse and apparently ambiguous, being based beyond the body, on the social relations among peers, their ancestors, and nature. Based on a qualitative study and a four-year stay in Mozambique, this article analyzes the discourses of patients and biomedical practitioners on traditional health care providers, i.e., tinyanga and zion pastors, linking them to local terminology of malaria, in a rural district in southern Mozambique. In the current context of therapeutic pluralism and high mobility, the lack of solidarity and compassion attributed to tinyanga is supported by the monetization and commodification of their medicinal rituals and knowledge, as well as by competition with other providers in attracting patients. The implementation of zion churches, of Christian nature and performing therapeutic practices similar to tinyanga, is presented as a local advantageous solution due to the strong community connection, the comfort and reciprocity among the members, and the therapeutic results at low cost. In terms of health care policies and clinical practice, the invisibility of zion pastors and the subordinate role of healers is managed according to interests, based on vague ideas and prejudices from biomedical providers. The implementation of health policies that address the local diversity, the existing power relations and medical knowledge and practices can strengthen the biomedical care services and harmonize relations between the providers and the population

Good Health, Quality Education, Sustainable Communities, Human Rights

The publication collects the contributions presented during the International Symposium of the Italian UNESCO Chairs (CONIUS) entitled Human Rights and Sustainable Development Goals 2030, which took place on 16 November 2018 at the University of Florence. The contributions of national and international experts address the Global Aims for Sustainable Development of the UNESCO including Sustainable Development Goals (SDGs) n. 3 Improvement of the ‘Global Health’, n. 4 ‘Quality Education’, n. 11 ‘Cities and Inclusive Human Sett lements’ and n. 16 ‘Peace and Justice’, using transdisciplinary and transnational perspectives and implemented through theoretical studies and good practices

Estimating the Number of Paediatric Fevers Associated with Malaria Infection Presenting to Africa's Public Health Sector in 2007

Peter Gething and colleagues compute the number of fevers likely to present to public health facilities in Africa and the estimated number of these fevers likely to be infected with Plasmodium falciparum malaria parasites

Integrating Semantic Knowledge to Tackle Zero-shot Text Classification

Insufficient or even unavailable training data of emerging classes is a big challenge of many classification tasks, including text classification. Recognising text documents of classes that have never been seen in the learning stage, so-called zero-shot text classification, is therefore difficult and only limited previous works tackled this problem. In this paper, we propose a two-phase framework together with data augmentation and feature augmentation to solve this problem. Four kinds of semantic knowledge (word embeddings, class descriptions, class hierarchy, and a general knowledge graph) are incorporated into the proposed framework to deal with instances of unseen classes effectively. Experimental results show that each and the combination of the two phases achieve the best overall accuracy compared with baselines and recent approaches in classifying real-world texts under the zero-shot scenario.Comment: Accepted NAACL-HLT 201

Data value and care value in the practice of health systems: A case study in Uganda.

In anthropology, interest in how values are created, maintained and changed has been reinvigorated. In this case study, we draw on this literature to interrogate concerns about the relationship between data collection and the delivery of patient care within global health. We followed a pilot study conducted in Kayunga, Uganda that aimed to improve the collection of health systems data in five public health centres. We undertook ethnographic research from July 2015 to September 2016 in health centres, at project workshops, meetings and training sessions. This included three months of observations by three fieldworkers; in-depth interviews with health workers (n = 15) and stakeholders (n = 5); and six focus group discussions with health workers. We observed that measurement, calculation and narrative practices could be assigned care-value or data-value and that the attempt to improve data collection within health facilities transferred 'data-value' into health centres with little consideration among project staff for its impact on care. We document acts of acquiescence and resistance to data-value by health workers. We also describe the rare moments when senior health workers reconciled these two forms of value, and care-value and data-value were enacted simultaneously. In contrast to many anthropological accounts, our analysis suggests that data-value and care-value are not necessarily conflicting. Actors seeking to make changes in health systems must, however, take into account local forms of value and devise health systems interventions that reinforce and enrich existing ethically driven practice