While progress has been made toward describing the need for ontology evaluation and offering proposals concerning what properties to measure and how, work remains to develop ontology evaluation as a ...rigorous discipline. Ontologies as information artifacts have a variety of aspects that can inform their evaluation, both in terms of what is evaluated and the metrics used. Ontology evaluation as a discipline requires (1) having a systematic account of the different aspects of ontologies and the properties relevant to those aspects, (2) critically developing methods for examining those properties, (3) developing comparative metrics that allow ontology engineers to compare the effects of various modeling choices and allow users to compare the merits of existing ontologies, and (4) charting possible pitfalls of evaluation. This paper considers various properties of ontologies that have been proposed and organizes these properties according to different aspects of ontologies. To begin bringing previous work together and to illustrate where pitfalls and potential solutions might enter into a rigorous evaluation, I offer a more in depth (though still partial) analysis of evaluating the correctness of ontologies. I conclude with a discussion of next steps in systematizing ontology evaluation.
Social media analysis has shown tremendous potential to understand public's opinion on a wide variety of topics. In this paper, we have mined Twitter to understand the public's perception of the ...Internet of Things (IoT). We first generated the discussion trends of the IoT from multiple Twitter data sources and validated these trends with Google Trends. We then performed sentiment analysis to gain insights of the public's attitude towards the IoT. As anticipated, our analysis indicates that the public's perception of the IoT is predominantly positive. Further, through topic modeling, we learned that public tweets discussing the IoT were often focused on business and technology. However, the public has great concerns about privacy and security issues toward the IoT based on the frequent appearance of related terms. Nevertheless, no unexpected perceptions were identified through our analysis. Our analysis was challenged by the limited fraction of tweets relevant to our study. Also, the user demographics of Twitter users may not be strongly representative of the population of the general public.
Full text
Available for:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Adverse childhood experiences (ACEs) are potentially traumatic exposures experienced during childhood, for example, neglect. There is growing evidence that the coronavirus disease 2019 (COVID-19) ...pandemic and related socioeconomic conditions contributed to an increased risk of ACEs. As public health programs/services are re-evaluated and restored following the state of emergency, it is important to plan using an ACEs-informed lens. The aim of this study was to identify and prioritize initiatives or activities that Public Health Ontario (PHO) could undertake to support Ontario public health units' work towards ACEs-informed pandemic recovery plans. The Child Health and Nutrition Research Initiative method was adapted to conduct a priority-setting exercise (May-October 2022). Two online surveys were administered with members of the Healthy Growth and Development (HGD) Evidence Network, comprised of public health unit staff working in child and family health/HGD from Ontario's 34 public health units. In the first survey, participants were asked to propose activities or initiatives that PHO could undertake to support Ontario public health units' work towards ACEs-informed planning. In the second survey, participants were asked to score the final list of options against pre-determined prioritization criteria (for example, relevance). Responses were numerically coded and used to calculate prioritization scores, which were used to rank the options. In all, 76% of public health units (n = 26) responded to the first survey to identify options. The 168 proposed ideas were consolidated into a final list of 13 options, which fall under PHO's scientific and technical support mandate areas (data and surveillance, evidence synthesis, collaboration and networking, knowledge exchange and research). A total of 79% of public health units (n = 27) responded to the follow-up survey to prioritize options. Prioritization scores ranged from 76.4% to 88.6%. The top-ranked option was the establishment of a new provincial ACEs community of practice. Over three quarters of public health units contributed to identifying and ranking 13 options for PHO to support public health units in considering and addressing ACEs through pandemic recovery planning. In consultation with the ACEs and Resilience Community of Practice, recently formed on the basis of this exercise, PHO will continue to use the ranked list of options to inform work-planning activities/priorities.
Full text
Available for:
IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
The symbiotic interactions that occur between humans and organisms in our environment have a tremendous impact on our health. Recently, there has been a surge in interest in understanding the complex ...relationships between the microbiome and human health and host immunity against microbial pathogens, among other things. To collect and manage data about these interactions and their complexity, scientists will need ontologies that represent symbiotic interactions as they occur in reality.
We began with two papers that reviewed the usage of 'symbiosis' and related terms in the biology and ecology literature and prominent textbooks. We then analyzed several prominent standard terminologies and ontologies that contain representations of symbiotic interactions, to determine if they appropriately defined 'symbiosis' and related terms according to current scientific usage as identified by the review papers. In the process, we identified several subtypes of symbiotic interactions, as well as the characteristics that differentiate them, which we used to propose textual and axiomatic definitions for each subtype of interaction. To both illustrate how to use the ontological representations and definitions we created and provide additional quality assurance on key definitions, we carried out a referent tracking analysis and representation of three scenarios involving symbiotic interactions among organisms.
We found one definition of 'symbiosis' in an existing ontology that was consistent with the vast preponderance of scientific usage in biology and ecology. However, that ontology changed its definition during the course of our work, and discussions are ongoing. We present a new definition that we have proposed. We also define 34 subtypes of symbiosis. Our referent tracking analysis showed that it is necessary to define symbiotic interactions at the level of the individual, rather than at the species level, due to the complex nature in which organisms can go from participating in one type of symbiosis with one organism to participating in another type of symbiosis with a different organism.
As a result of our efforts here, we have developed a robust representation of symbiotic interactions using a realism-based approach, which fills a gap in existing biomedical ontologies.
Full text
Available for:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
In 2009, the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) established the Pediatric Terminology Harmonization Initiative to establish a core library of ...terms to facilitate the acquisition and sharing of knowledge between pediatric clinical research, practice, and safety reporting. A coalition of partners established a Pediatric Terminology Adverse Event Working Group in 2013 to develop a specific terminology relevant to international pediatric adverse event (AE) reporting. Pediatric specialists with backgrounds in clinical care, research, safety reporting, or informatics, supported by biomedical terminology experts from the National Cancer Institute's Enterprise Vocabulary Services participated. The multinational group developed a working definition of AEs and reviewed concepts (terms, synonyms, and definitions) from 16 pediatric clinical domains. The resulting AE terminology contains >1000 pediatric diseases, disorders, or clinical findings. The terms were tested for proof of concept use in 2 different settings: hospital readmissions and the NICU. The advantages of the AE terminology include ease of adoption due to integration with well-established and internationally accepted biomedical terminologies, a uniquely temporal focus on pediatric health and disease from conception through adolescence, and terms that could be used in both well- and underresourced environments. The AE terminology is available for use without restriction through the National Cancer Institute's Enterprise Vocabulary Services and is fully compatible with, and represented in, the Medical Dictionary for Regulatory Activities. The terminology is intended to mature with use, user feedback, and optimization.
Successes of LLMs contrast with their inscrutability, inaccuracy, and hallucinations, which underwrite concerns over the reliability and trustworthiness of these systems, motivating investigations ...into commonsense reasoning, AI explainability, and formal verification techniques. ...proper assessments of hybrid machine learning/symbolic systems require novel strategies to facilitate comparisons of performance and guide future Al progress. ...many find it challenging to trust the outputs of model checkers and proof assistants for anything substantial. Altogether, these discussions made clear that AGI poses unique challenges for evaluation and assessment that go beyond measuring performance of a specific task.
Full text
Available for:
CEKLJ, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
The translational research community, in general, and the Clinical and Translational Science Awards (CTSA) community, in particular, share the vision of repurposing EHRs for research that will ...improve the quality of clinical practice. Many members of these communities are also aware that electronic health records (EHRs) suffer limitations of data becoming poorly structured, biased, and unusable out of original context. This creates obstacles to the continuity of care, utility, quality improvement, and translational research. Analogous limitations to sharing objective data in other areas of the natural sciences have been successfully overcome by developing and using common ontologies. This White Paper presents the authors’ rationale for the use of ontologies with computable semantics for the improvement of clinical data quality and EHR usability formulated for researchers with a stake in clinical and translational science and who are advocates for the use of information technology in medicine but at the same time are concerned by current major shortfalls. This White Paper outlines pitfalls, opportunities, and solutions and recommends increased investment in research and development of ontologies with computable semantics for a new generation of EHRs.
Sm proteins form stable ribonucleoprotein (RNP) complexes with small nuclear (sn)RNAs and are core components of the eukaryotic spliceosome. In vivo, the assembly of Sm proteins onto snRNAs requires ...the survival motor neurons (SMN) complex. Several reports have shown that SMN protein binds with high affinity to symmetric dimethylarginine (sDMA) residues present on the C-terminal tails of SmB, SmD1, and SmD3. This post-translational modification is thought to play a crucial role in snRNP assembly. In human cells, two distinct protein arginine methyltransferases (PRMT5 and PRMT7) are required for snRNP biogenesis. However, in Drosophila, loss of Dart5 (the fruit fly PRMT5 ortholog) has little effect on snRNP assembly, and homozygous mutants are completely viable. To resolve these apparent differences, we examined this topic in detail and found that Drosophila Sm proteins are also methylated by two methyltransferases, Dart5/PRMT5 and Dart7/PRMT7. Unlike dart5, we found that dart7 is an essential gene. However, the lethality associated with loss of Dart7 protein is apparently unrelated to defects in snRNP assembly. To conclusively test the requirement for sDMA modification of Sm proteins in Drosophila snRNP assembly, we constructed a fly strain that exclusively expresses an isoform of SmD1 that cannot be sDMA modified. Interestingly, these flies were viable, and snRNP assays revealed no defects in comparison to wild type. In contrast, dart5 mutants displayed a strong synthetic lethal phenotype in the presence of a hypomorphic Smn mutation. We therefore conclude that dart5 is required for viability when SMN is limiting.
The durability of immune memory after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) messenger RNA (mRNA) vaccination remains unclear. In this study, we longitudinally profiled vaccine ...responses in SARS-CoV-2–naïve and –recovered individuals for 6 months after vaccination. Antibodies declined from peak levels but remained detectable in most subjects at 6 months. By contrast, mRNA vaccines generated functional memory B cells that increased from 3 to 6 months postvaccination, with the majority of these cells cross-binding the Alpha, Beta, and Delta variants. mRNA vaccination further induced antigen-specific CD4
and CD8
T cells, and early CD4
T cell responses correlated with long-term humoral immunity. Recall responses to vaccination in individuals with preexisting immunity primarily increased antibody levels without substantially altering antibody decay rates. Together, these findings demonstrate robust cellular immune memory to SARS-CoV-2 and its variants for at least 6 months after mRNA vaccination.
PDF
