Coordinating Coronavirus Research: The COVID-19 Infectious Disease Ontology

Rapidly, accurately and easily interpreting generated data is of fundamental concern. Ontologies – structured controlled vocabularies – support interoperability and prevent the development of data silos which undermine interoperability. The Open Biological and Biomedical Ontologies (OBO) Foundry serves to ensure ontologies remain interoperable through adherence by its members to core ontology design principles. For example, the Infectious Disease Ontology (IDO) Core includes terminological content common to investigations of all infectious diseases. Ontologies covering more specific infectious diseases in turn extend from IDOCore, such as the Coronavirus Infectious Disease Ontology (CIDO). The growing list of virus-specific IDO extensions has motivated construction of a reference ontology covering content common to viral infectious disease investigations: the Virus Infectious Disease Ontology (VIDO). Additionally the present pandemic has motivated construction of a more specific extension of CIDO covering terminological contents specific to the pandemic: the COVID-19 Infectious Disease Ontology (IDO-COVID-19). We report here the development of VIDO and IDO-COVID-19. More specifically we examine newly minted terms for each ontology, showcase reuse of terms from existing OBO ontologies, motivate choicepoints for ontological decisions based on research from relevant life sciences, apply ontology terms to explicate viral pathogenesis, and discuss the annotating power of virus ontologies for use in machine-learning projects

Coordinating virus research: The Virus Infectious Disease Ontology

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects

Status of Exosphaeroma amplicauda (Stimpson, 1857), E-aphrodita (Boone, 1923) and description of three new species (Crustacea, Isopoda, Sphaeromatidae) from the north-eastern Pacific

Exosphaeroma amplicauda (Stimpson, 1857) from the west coast of North America is reviewed and redescribed and revealed to be a group of closely related species. A neotype is designated and the species redescribed based on the neotype and topotypic specimens. Exosphaeroma amplicauda is known only from the coast of California, at Marin, Sonoma and San Mateo Counties. E. aphrodita (Boone, 1923), type locality La Jolla, California and previously considered nomen dubium is taken out of synonymy and re-validated. A further three species: E. paydenae sp. n., E. russellhansoni sp. n., and E. pentcheffi sp. n. are described herein. Sphaeroma octonctum Richardson, 1899 is placed into junior synonymy with Exosphaeroma amplicauda. A key to the Pacific West Coast Exosphaeroma is provided

A Supreme Challenge: Reducing Judicial Reliance on the Plenary Power Doctrine in Immigration Law

Part One of the paper provides the background of the plenary power doctrine and reviews the evolution of immigration law over the subsequent century in light of the doctrine. Part Two discusses the Ma and Zadyvdas decisions in the lower courts as examples of both the schizophrenic nature of immigration jurisprudence and evidence of the necessity for the Supreme Court to narrow the use of the plenary power doctrine

Environmental burden of childhood disease in Europe

Background: Environmental factors determine children's health. Quantifying the health impacts related to environmental hazards for children is essential to prioritize interventions to improve health in Europe. Objective: This study aimed to assess the burden of childhood disease due to environmental risks across the European Union. Methods: We conducted an environmental burden of childhood disease assessment in the 28 countries of the EU (EU28) for seven environmental risk factors (particulate matter less than 10 micrometer of diameter (PM10) and less than 2.5 micrometer of diameter (PM2.5), ozone, secondhand smoke, dampness, lead, and formaldehyde). The primary outcome was disability-adjusted life years (DALYs), assessed from exposure data provided by the World Health Organization, Global Burden of Disease project, scientific literature, and epidemiological risk estimates. Results: The seven studied environmental risk factors for children in the EU28 were responsible for around 211,000 DALYs annually. Particulate matter (PM10 and PM2.5) was the main environmental risk factor, producing 59% of total DALYs (125,000 DALYs), followed by secondhand smoke with 20% of all DALYs (42,500 DALYs), ozone 11% (24,000 DALYs), dampness 6% (13,000 DALYs), lead 3% (6200 DALYs), and formaldehyde 0.2% (423 DALYs). Conclusions: Environmental exposures included in this study were estimated to produce 211,000 DALYs each year in children in the EU28, representing 2.6% of all DALYs in children. Among the included environmental risk factors, air pollution (particulate matter and ozone) was estimated to produce the highest burden of disease in children in Europe, half of which was due to the effects of PM10 on infant mortality. Effective policies to reduce environmental pollutants across Europe are needed.The research leading to these results received funding from the European Community’s Seventh Framework Programme (FP7/2007–2013) under grant agreement no 308333—the HELIX project

Particle Emissions from Aircraft Engines–A Survey of the European Project PartEmis

An overview of the goals and achievements of the European PartEmis project (Measurement and prediction of emissions of aerosols and gaseous precursors from gas turbine engines) is presented. PartEmis was focussed on the characterisation and quantification of exhaust emissions from a gas turbine engine. The engine was composed of a combustor and a unit to simulate a 3-shaft turbine section (so-called Hot End Simulator; HES). A comprehensive suite of aerosol, gas and chemi-ion measurements were conducted under different, i) combustor and HES operating conditions, ii) fuel sulphur concentrations. Measured aerosol properties were mass and number concentration, size distribution, mixing state, thermal stability of internally mixed particles, hygroscopicity, cloud condensation nuclei (CCN) activation potential, and chemical composition. Furthermore, chemi-ions, non-methane volatile organic compounds (NMVOCs) and OH were monitored. The combustor operation conditions corresponded to modern and older engine gas path temperatures at cruise altitude, with fuel sulphur contents (FSC) of 0.05, 0.41, and 1.270 g kg−1. The combustor behaved like a typical aircraft engine combustor with respect to thermodynamic data and main emissions, which suggests that the PartEmis database may be applicable to contemporary aircraft engines. The conclusions drawn from the PartEmis experiment are discussed separately for combustion particles, ultrafine particles, sulphate-containing species and chemi-ions, particle hygrioscopic growth and CCN activation, gaseous organic fraction, and emission properties

Coordinating virus research: The Virus Infectious Disease Ontology.

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies-structured, controlled, vocabularies-are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects

Design and structure-activity relationships of potent and selective inhibitors of undecaprenyl pyrophosphate synthase (UPPS): tetramic, tetronic acids and dihydropyridin-2-ones.

Based on a pharmacophore hypothesis substituted tetramic and tetronic acid 3-carboxamides as well as dihydropyridin-2-one-3-carboxamides were investigated as inhibitors of undecaprenyl pyrophosphate synthase (UPPS) for use as novel antimicrobial agents. Synthesis and structure-activity relationship patterns for this class of compounds are discussed. Selectivity data and antibacterial activities for selected compounds are provided

Relationships among BFO, GO, OGMS, IDO Core, the Cell Ontology (CL), VIDO, the Common Core Ontology (CCO), OBI, IAO, the Uber-Anatomy Ontology (UBERON), CIDO, ChEBI, PRO (Protein Ontology), and PTRANS.

Relationships among BFO, GO, OGMS, IDO Core, the Cell Ontology (CL), VIDO, the Common Core Ontology (CCO), OBI, IAO, the Uber-Anatomy Ontology (UBERON), CIDO, ChEBI, PRO (Protein Ontology), and PTRANS.</p