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Mondo: integrating disease terminology across communities

Precision medicine aims to enhance diagnosis, treatment, and prognosis by integrating multimodal data at the point of care. However, challenges arise due to the vast number of diseases, differing methods of classification, and conflicting terminological coding systems and practices used to represent molecular definitions of disease. This lack of interoperability artificially constrains the potential for diagnosis, clinical decision support, care outcome analysis, as well as data linkage across research domains to support the development or repurposing of therapeutics. There is a clear and pressing need for a unified system for managing disease entities⁠—including identifiers, synonyms, and definitions. To address these issues, we created the Mondo disease ontology—a community-driven, open-source, unified disease classification system that harmonizes diverse terminologies into a consistent, computable framework. Mondo integrates key medical and biomedical terminologies, including Online Mendelian Inheritance in Man (OMIM), Orphanet, Medical Subject Headings (MeSH), National Cancer Institute Thesaurus (NCIt), and more, to provide a comprehensive and accurate representation of disease concepts with fully provenanced and attributed links back to the sources. Mondo can be used as the handle for curation of gene–disease associations utilized in diagnostic applications, research applications such as computational phenotyping, and in clinical coding systems in clinical decision support by pointing the clinician to the numerous knowledge resources linked to the Mondo identifier. Mondo's community-centric approach, stewarded by the Monarch Initiative's expertise in ontologies, ensures that the ontology remains adaptable to the evolving needs of biomedical research and clinical communities, as well as the knowledge providers.

biomedical informatics↗

PETSc/TAO Users Manual Revision 3.25

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations (PDEs) and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for implementing large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Nuisance Odors: Is there a Concern - 12340

Nuisance odors are generally thought of as just being annoying or unpleasant and not causing any physiological harm to our internal organs or other biologic systems. Yet during an excavation of buried animal remains, field workers experienced a multitude of symptoms that are associated with exposures to toxic materials. An examination of the decomposition process revealed that there is a potential off-gassing of a number of common, yet harmful chemicals including ammonia, mercaptans, hydrogen sulfide, butyric acid and phenol. In addition, other compounds, that have limited information such as established health data and occupational exposure limits, were also potential contaminants-of-concern. While a variety of monitoring and sampling techniques were used to assess worker exposures, all results indicated non-detectable airborne concentrations. Nevertheless, workers were experiencing such symptoms as nausea and headaches. As such, protective measures were necessary for field personnel to continue work while having confidence that the project was instituting sincere steps to ensure their health and safety. Researching the possible reasons for the causes of workers exhibiting adverse health effects from nuisance odors revealed that such exposures initiate electrochemical pathways, starting from the olfactory bulb to the brain, followed by a transfer of information to such biologic systems as the hypothalamus and pituitary gland. These systems, in turn, secrete hormones that cause a number of involuntary reactions; many of which are observed as typical adverse health effects, when in fact, they are merely reactions caused by the brain's memory; most likely created from previous experiences to unpleasant odors. The concern then focuses of how the Occupational Safety and Health community shall respond to such workplace exposures. Future work in this area may need to focus on the viability of current occupational exposure limits and the possibility of revising these standards. Another area of consideration would be whether nuisance odors will need separate and distinct criteria with regards to hazard identification and control. While evidence suggests that odorants do not cause direct toxicological effects to the various biologic systems, they can be influential by initiating symptoms that are associated with known toxins. The difference between the classic toxic systemic reactions and those initiated by nuisance odors can be summarized as one causing a dysfunction of a target organ or system as opposed to triggering a message to the brain which causes a physical reaction. While strong odors may exist at HAZWOPER work sites, their particular risk of pathogenic disease has yet to be established. This leaves many unanswered questions; the most obvious being, 'can an odorous chemical that can result in headaches, nausea, changes in blood pressure, body temperature, etc., be considered a toxin even if biological systems remain unaffected and sampling/monitoring protocol negative stimuli, thereby causing symptomatic experiences; will such disciplines as psychology need to be considered as part of the expertise within the field a environmental and occupational health? In the classic text, 'The Fundamentals of Industrial Hygiene' industrial hygiene has been defined as 'that science and art devoted to the anticipation, recognition, evaluation, and control of those environmental factors or stressors arising in or from the workplace that may cause sickness, impaired health and well-being, or significant discomfort among workers or among the citizens of the community'. Based on this definition, it is indeed the responsibility of the occupational health professional to move forward and to provide an effective program to 'anticipate, recognize, evaluate, and control' such airborne contaminants that may not be adequately controlled based on current knowledge and technology. The question is, 'Is the industrial hygiene community equipped to carry out this responsibility?' 'Are new assessment methods and tools necessary? Are alternate exposure limits needed and can they be adequately implemented? As more of the non-traditional health hazards become recognized, it appears that it shall be essential for more sophisticated methods to be part of the standard practice used to assess human health. Whether that means more sensitive equipment that has greater detection capabilities, or the development of new technologies designed specifically for these hazards, at present can only be left to speculation. While the occupational health community may wrestle with these questions, the responsibility of the safety and health community must maintain its diligence. As such, persons within the discipline of environmental and occupational health must continue to communicate the hazards and controls to the work force. Through such efforts, the workforce shall become engaged in the process of hazard identification, assessment and control, which, in turn, will create a greater appreciation and acceptance for field assessment methods as well as the processes by which workplace controls are designed to protect them. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗