The range scheduling aid

The Air Force Space Command schedules telemetry, tracking and control activities across the Air Force Satellite Control network. The Range Scheduling Aid (RSA) is a rapid prototype combining a user-friendly, portable, graphical interface with a sophisticated object-oriented database. The RSA has been a rapid prototyping effort whose purpose is to elucidate and define suitable technology for enhancing the performance of the range schedulers. Designing a system to assist schedulers in their task and using their current techniques as well as enhancements enabled by an electronic environment, has created a continuously developing model that will serve as a standard for future range scheduling systems. The RSA system is easy to use, easily ported between platforms, fast, and provides a set of tools for the scheduler that substantially increases his productivity

Status of Tree Snails (Gastropoda: Partulidae) on Guam, with a Resurvey of Sites Studied by H. E. Campton in 1920

Tree snails of the family Partulidae have declined on Guam since World War II. One species, indigenous to the western Pacific, Partula radiolata, is still locally common along stream courses in southern areas of the island. The Mariana Island endemic Samoana fragilis is present but not found in abundance anywhere on Guam. Partula gibba, another Mariana endemic, is currently known only from one isolated coastal valley along the northwestern coast, and appears to be in a state of decline. The Guam endemic Partula salifana was not found in areas where it had been previously collected by earlier researchers, and is thus believed to be extinct. The decline and extinction of these snails are related to human activities. The single most important factor is likely predation by snails that were introduced as biological control agents for the giant African snail, Achatina fulica. The current, most serious threat is probably the introduced flatworm Platydemus manokwari. This flatworm is also the likely cause of extinctions of other native and introduced gastropods on Guam and may be the most important threat to the Mariana Partulidae

Functions in Basic Formal Ontology

The notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application to domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each of the categories identified and defined by a top-level ontology is integrated with the others in a coherent fashion. Basic Formal Ontology (BFO) has from the beginning included function as one of its categories, exploiting a version of the etiological account of function that is framed at a level of generality sufficient to accommodate both biological and artifactual functions. This account has been subjected to a series of criticisms and refinements. We here articulate BFO’s account of function, provide some reasons for favoring it over competing views, and defend it against objections

Ontologies for the study of neurological disease

We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level candidate OBO Foundry ontology that provides a set of general classes that can be used to describe general aspects of medical science. ND is being built with classes utilizing both textual and axiomatized definitions that describe and formalize the relations between instances of other classes within the ontology itself as well as to external ontologies such as the Gene Ontology, Cell Ontology, Protein Ontology, and Chemical Entities of Biological Interest. In addition, references to similar or associated terms in external ontologies, vocabularies and terminologies are included when possible. Initial work on ND is focused on the areas of Alzheimer’s and other diseases associated with dementia, multiple sclerosis, and stroke and cerebrovascular disease. Extensions to additional groups of neurological diseases are planned. The second ontology, the Neuro-Psychological Testing Ontology (NPT), is intended to provide a set of classes for the annotation of neuropsychological testing data. The intention of this ontology is to allow for the integration of results from a variety of neuropsychological tests that assay similar measures of cognitive functioning. Neuro-psychological testing is an important component in developing the clinical picture used in the diagnosis of patients with a range of neurological diseases, such as Alzheimer’s disease and multiple sclerosis, and following stroke or traumatic brain injury. NPT is being developed as an extension to the Ontology for Biomedical Investigations

The Plant Ontology: A common reference ontology for plants

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms

Chapter 2.2: 3-D Topo Surface Visualization of Metal Ion Anti-Buffering: An Unexpected Behavior in Metal–Ligand Complexation Systems

Diluting a system that contains metal complexes can sometimes cause surprises. This chapter describes “metal ion anti-buffering”, a situation in which free metal ion concentrations rapidly increase as system dilution drives dissociation. It only occurs under excess free ligand conditions when a solution is dominated by higher stoichiometry complexes. The Law of Mass Action is used to provide a mathematical justification for the phenomenon. A Cu2+-ethylenediamine mixture exhibits this phenomenon when excess free ethylenediamine (en) is present. For example, it occurs when diluting a solution containing a four-fold excess of en over Cu2+. As this mixture is diluted by a factor of ~5600, the modeled free Cu2+ concentration shows a ~470-fold increase. Taken together, this is 2.5 million times higher than dilution of the system would yield in other circumstances. Included are experimental data confirming anti-buffering in the Cu2+-en system. Many other metal-ligand systems can display this behavior. Four additional examples are illustrated including an amino acid under physiological pHs. Anti-Buffering TOPOS, a downloadable Excel workbook in a supplemental file, allows readers to simulate this behavior for many metal-ligand systems. A PowerPoint lecture and teaching materials are also provided, suitable for inclusion in upper division and graduate courses in analytical chemistry, biochemistry and geochemistry.https://scholarworks.umt.edu/topos/1005/thumbnail.jp

An improved ontological representation of dendritic cells as a paradigm for all cell types

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’

Biomedical Informatics and Granularity

An explicit formal-ontological representation of entities existing at multiple levels of granularity is an urgent requirement for biomedical information processing. We discuss some fundamental principles which can form a basis for such a representation. We also comment on some of the implicit treatments of granularity in currently available ontologies and terminologies (GO, FMA, SNOMED CT)