An Ontology-Based Framework for Clinical Research Databases

The Ontology-Based eXtensible data model (OBX) was developed to serve as a framework for the development of a clinical research database in the Immunology Database and Analysis Portal (ImmPort) system. OBX was designed around the logical structure provided by the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). By using the logical structure provided by these two well-formulated ontologies, we have found that a relatively simple, extensible data model could be developed to represent the relatively complex domain of clinical research. In addition, the common framework provided by the BFO should make it straightforward to utilize OBX database data dictionaries based on reference and application ontologies from the OBO Foundry

Ontology-based knowledge representation of experiment metadata in biological data mining

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes

Tethered balloon-borne profile measurements of atmospheric properties in the cloudy atmospheric boundary layer over the Arctic sea ice during MOSAiC: Overview and first results

The tethered balloon-borne measurement system BELUGA (Balloon-bornE moduLar Utility for profilinG the lower Atmosphere) was deployed over the Arctic sea ice for 4 weeks in summer 2020 as part of the Multidisciplinary drifting Observatory for the Study of Arctic Climate expedition. Using BELUGA, vertical profiles of dynamic, thermodynamic, aerosol particle, cloud, radiation, and turbulence properties were measured from the ground up to a height of 1,500 m. BELUGA was operated during an anomalously warm period with frequent liquid water clouds and variable sea ice conditions. Three case studies of liquid water phase, single-layer clouds observed on 3 days (July 13, 23, and 24, 2020) are discussed to show the potential of the collected data set to comprehensively investigate cloud properties determining cloud evolution in the inner Arctic over sea ice. Simulated back-trajectories show that the observed clouds have evolved within 3 different air masses (“aged Arctic,” “advected over sea ice,” and “advected over open ocean”), which left distinct fingerprints in the cloud properties. Strong cloud top radiative cooling rates agree with simulated results of previous studies. The weak warming at cloud base is mostly driven by the vertical temperature profile between the surface and cloud base. In-cloud turbulence induced by the cloud top cooling was similar in strength compared to former studies. From the extent of the mixing layer, it is speculated that the overall cloud cooling is stronger and thus faster in the warm oceanic air mass. Larger aerosol particle number concentrations and larger sizes were observed in the air mass advected over the sea ice and in the air mass advected over the open ocean

Experiment Transcripts for the Evaluation of the Rational Environment

This report supplements the report Evaluation of the Rational Environment. It contains the instantiation of the experiments presented in Evaluation of ADA Environments (CMU/SEI-87-TR-001, by Nelson Weiderman, N., et al.). Overall conclusions and analysis of the Rational Environment can be found in Evaluation of the Rational Environment