Cross-Product Extensions of the Gene Ontology

The Gene Ontology is being normalized and extended to include computable logical definitions. These definitions are partitioned into mutually exclusive cross-product sets, many of which reference other OBO Foundry ontologies. The results can be used to reason over the ontology, and to make cross-ontology queries

Evaluation Findings: School and Workplace Strategies 2005-2007

This report is an evaluation developed to provide updates on the progress of the Missouri Foundation for Health’s Tobacco Prevention and Cessation Initiative (TPCI). The report provides an overview of the activities and outcomes regarding school and workplace strategies that occurred between 2005 and 2007.https://openscholarship.wustl.edu/cphss/1099/thumbnail.jp

Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.

BACKGROUND: The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes. To facilitate accurate and consistent systems-wide biological representation, it is necessary to integrate the chemical view of these entities with the biological view of GO functions and processes. We describe a collaborative effort between the GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure that the representation of chemicals in the GO is both internally consistent and in alignment with the chemical expertise captured in ChEBI. RESULTS: We have examined and integrated the ChEBI structural hierarchy into the GO resource through computationally-assisted manual curation of both GO and ChEBI. Our work has resulted in the creation of computable definitions of GO terms that contain fully defined semantic relationships to corresponding chemical terms in ChEBI. CONCLUSIONS: The set of logical definitions using both the GO and ChEBI has already been used to automate aspects of GO development and has the potential to allow the integration of data across the domains of biology and chemistry. These logical definitions are available as an extended version of the ontology from http://purl.obolibrary.org/obo/go/extensions/go-plus.owl

Annotation of gene product function from high-throughput studies using the Gene Ontology.

High-throughput studies constitute an essential and valued source of information for researchers. However, high-throughput experimental workflows are often complex, with multiple data sets that may contain large numbers of false positives. The representation of high-throughput data in the Gene Ontology (GO) therefore presents a challenging annotation problem, when the overarching goal of GO curation is to provide the most precise view of a gene's role in biology. To address this, representatives from annotation teams within the GO Consortium reviewed high-throughput data annotation practices. We present an annotation framework for high-throughput studies that will facilitate good standards in GO curation and, through the use of new high-throughput evidence codes, increase the visibility of these annotations to the research community

Engaging stakeholders to inform national implementation of critical time intervention in a program serving homeless-experienced Veterans

The Veterans Affairs (VA) Grant and Per Diem Case Management “Aftercare” program provides 6 months of case management for homeless-experienced Veterans (HEVs) transitioning to permanent housing, with the aim of decreasing returns to homelessness. Implementing Critical Time Intervention (CTI)—an evidence-based case management practice—would standardize care across the 128 community-based agencies that provide Aftercare services. To prepare for national CTI implementation in Aftercare, guided by Replicating Effective Programs (REP), we conducted a four-site pilot in which we adapted a CTI implementation package (training, technical assistance, and external facilitation); characterized stakeholder perspectives regarding the acceptability and appropriateness of this package; and identified contextual factors that affected CTI implementation. We engaged a stakeholder workgroup to tailor existing CTI training and technical assistance materials for Aftercare. To provide tailored support for providers and leaders to adopt and incorporate evidence-based practices (EBPs) into routine care, we also developed external facilitation materials and processes. Over 9 months, we implemented this package at four sites. We conducted semi-structured interviews at pre-implementation, mid-implementation, and 6 months post-implementation, with HEVs (n = 37), case managers (n = 16), supervisors (n = 10), and VA leaders (n = 4); these data were integrated with templated reflection notes from the project facilitator. We used rapid qualitative analysis and targeted coding to assess the acceptability and appropriateness of CTI and our implementation package and identify factors influencing CTI implementation. Stakeholders generally found CTI acceptable and appropriate; there was consensus that components of CTI were useful and compatible for this setting. To adapt our implementation package for scale-up, this pilot highlighted the value of robust and tangible CTI training and technical assistance—grounded in real-world cases—that highlights the congruence of CTI with relevant performance metrics. Variations in agency-level contextual factors may necessitate more intense and tailored supports to implement and sustain complex EBPs like CTI. Processes used in this pilot are relevant for implementing other EBPs in organizations that serve vulnerable populations. EBP scale-up and sustainment can be enhanced by engaging stakeholders to tailor EBPs for specific contexts; pilot testing and refining implementation packages for scale-up; and using qualitative methods to characterize contextual factors that affect EBP implementation

High resolution mapping and positional cloning of ENU-induced mutations in the Rw region of mouse chromosome 5

<p>Abstract</p> <p>Background</p> <p>Forward genetic screens in mice provide an unbiased means to identify genes and other functional genetic elements in the genome. Previously, a large scale ENU mutagenesis screen was conducted to query the functional content of a ~50 Mb region of the mouse genome on proximal Chr 5. The majority of phenotypic mutants recovered were embryonic lethals.</p> <p>Results</p> <p>We report the high resolution genetic mapping, complementation analyses, and positional cloning of mutations in the target region. The collection of identified alleles include several with known or presumed functions for which no mutant models have been reported (<it>Tbc1d14</it>, <it>Nol14</it>, <it>Tyms</it>, <it>Cad</it>, <it>Fbxl5</it>, <it>Haus3</it>), and mutations in genes we or others previously reported (<it>Tapt1</it>, <it>Rest</it>, <it>Ugdh</it>, <it>Paxip1</it>, <it>Hmx1, Otoe, Nsun7</it>). We also confirmed the causative nature of a homeotic mutation with a targeted allele, mapped a lethal mutation to a large gene desert, and localized a spermiogenesis mutation to a region in which no annotated genes have coding mutations. The mutation in <it>Tbc1d14 </it>provides the first implication of a critical developmental role for RAB-GAP-mediated protein transport in early embryogenesis.</p> <p>Conclusion</p> <p>This collection of alleles contributes to the goal of assigning biological functions to all known genes, as well as identifying novel functional elements that would be missed by reverse genetic approaches.</p

Quality of chronic disease care in general practice: the development and validation of a provider interview tool

BACKGROUND: This article describes the development and psychometric evaluation of an interview instrument to assess provider-reported quality of general practice care for patients with diabetes, cardiovascular disease and asthma – the Australian General Practice Clinical Care Interview (GPCCI). METHODS: We administered the GPCCI to 28 general practitioners (family physicians) in 10 general practices. We conducted an item analysis and assessed the internal consistency of the instrument. We next assessed the quality of care recorded in the medical records of 462 of the general practitioners' patients with Type 2 diabetes, ischaemic heart disease/hypertension and/or moderate to severe asthma. This was then compared with results of the GPCCI for each general practice. RESULTS: Good internal consistency was found for the overall GPCCI (Cronbach's alpha = 0.75). As far as the separate sub-scales were concerned, diabetes had good internal consistency (0.76) but the internal consistency of the heart disease and asthma subscales was not strong (0.49 and 0.16 respectively). There was high inter-rater reliability of the adjusted scores of data extracted from patients' medical notes for each of the three conditions. Correlations of the overall GPCCI and patients' medical notes audit, combined across the three conditions and aggregated to practice level, showed that a strong relationship (r = 0.84, p = 0.003) existed between the two indices of clinical care. CONCLUSION: This study suggests that the GPCCI has good internal consistency and concurrent validity with patients' medical records in Australian general practice and warrants further evaluation of its properties, validity and utility

TNOs are cool: a survey of the transneptunian region

Over one thousand objects have so far been discovered orbiting beyond Neptune. These trans-Neptunian objects (TNOs) represent the primitive remnants of the planetesimal disk from which the planets formed and are perhaps analogous to the unseen dust parent-bodies in debris disks observed around other main-sequence stars. The dynamical and physical properties of these bodies provide unique and important constraints on formation and evolution models of the Solar System. While the dynamical architecture in this region (also known as the Kuiper Belt) is becoming relatively clear, the physical properties of the objects are still largely unexplored. In particular, fundamental parameters such as size, albedo, density and thermal properties are difficult to measure. Measurements of thermal emission, which peaks at far-IR wavelengths, offer the best means available to determine the physical properties. While Spitzer has provided some results, notably revealing a large albedo diversity in this population, the increased sensitivity of Herschel and its superior wavelength coverage should permit profound advances in the field. Within our accepted project we propose to perform radiometric measurements of 139 objects, including 25 known multiple systems. When combined with measurements of the dust population beyond Neptune (e.g. from the New Horizons mission to Pluto), our results will provide a benchmark for understanding the Solar debris disk, and extra-solar ones as well