Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain

Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have been there most thoroughly addressed. We advance a proposal resting on a distinction of three levels too often run together in biomedical ontology research: 1. the level of reality; 2. the level of cognitive representations of this reality; 3. the level of textual and graphical artifacts. We propose a reference terminology for ontology research and development that is designed to serve as common hub into which the several competing disciplinary terminologies can be mapped. We then justify our terminological choices through a critical treatment of the ‘concept orientation’ in biomedical terminology research

AN EMPIRICAL STUDY OF COMMUNITY AND FAMILY INTERVENTIONS TO PROMOTE PHYSICAL ACTIVITY AMONG LATINO YOUTH

Physical inactivity contributes to risks for chronic disease and premature death (World Health Organization, 2010). Community coalitions play an important role in addressing and preventing chronic diseases (Butterfoss, Goodman, & Wandersman, 1993). This dissertation examines two intervention efforts related to the Latino Health for All Coalition's action plan, using an ecological perspective (McLeroy, Bibeau, Steckler, & Glanz, 1988). The first study involved a universal intervention to promote physical activity among Latino boys and girls (age 5-15) in Kansas City by offering structured soccer sessions consisting of soccer drills and informal games. These structured soccer sessions were promoted though an informal, flyer-based campaign. An empirical case study design and related measures were used to answer four questions: 1) How effective was the campaign in attracting overweight and obese Latino youth? (involved analysis of a paper-and-pencil survey by parents of participating youth), 2) How frequently did participants attend? (involved analysis of weekly attendance records), 3) How much moderate-to-vigorous physical activity did participants accumulate during these informal soccer sessions? (involved the use of Actigraph accelerometers), and 4) How satisfied were parents and youth with these physical activity opportunities? (involved analysis of a paper-and-pencil survey at the concluding session). Results show that 74 youth attended at least one of the weekly soccer sessions (90.5% Hispanic/Latino, 43.2% overweight or obese). On average, youth attended 4.2 sessions; there was no difference in attendance rate by gender (t(40)=2.08, p=0.48) or body mass index category [F(2, 49) = 0.16, p = 0.85]. A convenience sample of 12 participants accumulated 18.8 to 22.2 minutes of moderate-to-vigorous physical activity during a single soccer session. Both children and parents expressed high levels of satisfaction with the structured soccer sessions. In conclusion, these structured soccer sessions enabled a diverse group of Latino children and youth to accumulate about a third of their daily requirement of physical activity, in an enjoyable way. The second study examined a targeted family-based intervention to promote physical activity in home settings. It involved Latino children (3 boys, 2 girls), ages 5 to 7. The intervention occurred during the summer (June - August). Parents were taught to set weekly physical activity goals for their children, develop weekly behavioral contracts, and reinforce short bouts of physical activity. Children wore Actigraph accelerometers during waking hours to monitor changes in physical activity levels. The U.S. Department of Health and Human Services guidelines for physical activity were reviewed with parents, followed by weekly accelerometer feedback on their child's physical activity level. A multiple baseline design was used to examine the effects of the intervention on daily levels of moderate-to-vigorous physical activity. The intervention resulted in large changes in physical activity for one participant and minimal increases in daily levels of moderate-to-vigorous physical activity for three of the remaining four participants. Factors that explain the variance in initial increase in physical activity (e.g., the home and neighborhood environment) were explored. Parents were able to implement most intervention components well, with the exception of their ability to consistently reinforce 10-minute bouts of physical activity. Finally parents expressed high levels of satisfaction with the intervention. Targeted interventions that train parents to set goals and develop behavioral contracts show promise for increasing the physical activity levels of children. Future research is needed to determine the longer-term effects of such interventions. Finally, this dissertation study provides an initial assessment of the Latino Health for All Coalition using preliminary measures of process outcomes (e.g., partners engaged, interventions developed). The coalition's effects were explored across all ecological levels--individual, family, organizational, community--posed by McLeroy et al. (1988). Health-based community coalitions can play an important role in assuring the prevention of chronic diseases for all groups within the community

ANALYZING THE EFFECTS OF COLLABORATIVE EFFORTS TO PREVENT CHILD SEXUAL ABUSE IN MINNESOTA

This study analyzes the effects of a community and state level effort to prevent CSA. Stop It Now! Minnesota, a CSA prevention initiative, received a grant from the U.S. Centers for Disease Control and Prevention to implement a multi-component intervention to prevent CSA. Stop It Now! Minnesota's intervention (the independent variable) trained adults to recognize and respond to the warning signs of CSA and provided support and services for potential perpetrators of CSA. The analysis examined three outcomes. Stop It Now! Minnesota documented their efforts to create community/system change (new or modified community programs, policies, and practices). Rates and types of change were analyzed. Second, records of calls from Minnesota to a national Helpline were reviewed. Call volume and type served as a measure of population-level preventative behavior. Third, annual child maltreatment reports were reviewed to examine rates of CSA reports to the Minnesota Department of Human Services. Results showed that Stop It Now! Minnesota facilitated numerous changes to the environment to prevent child sexual abuse. Preventative behavior in the form of Helpline calls increased, and reports of CSA in Minnesota decreased. These results suggest that Stop It Now! Minnesota's intervention was successful in preventing CSA. Implications for future research and practice are discussed

Practical experiences in concurrent, collaborative ontology building using Collaborative Protégé

Creation of an ontology according to some common plan is best accomplished collaboratively. This is sometimes contradicted by the distribution of the ontology’s developers. An obvious solution therefore is to build collaboration into ontology development tools. Such support necessarily includes both the technical means to perform editing operations upon an ontology, but also support for the communication that makes collaboration such a vital part of much ontology development. To investigate the distributed, collaborative ontology engineering process and the corresponding capabilities of the Collaborative Protege 3 (CP) tool, members of the OntoGenesis network came together and enriched the Ontology of Biomedical Investigations (OBI) with new content. The communications and interactions of the participants with each other, directly or through the tool, were tracked and analyzed. Our initial analysis of the degree to which this new tool fulfills the practical requirements of collaborative ontology engineering suggests the approach is promising. We present some observations and recommendations for CP based upon this experience

MIREOT: the Minimum Information to Reference an External Ontology Term

While the Web Ontology Language (OWL) provides a mechanism to import ontologies, this mechanism is not always suitable. First, given the current state of editing tools and the issues they have working with large ontologies, direct OWL imports have sometimes proven impractical for day-to-day development. Second, ontologies chosen for integration may be under active development and not aligned with the chosen design principles. Importing heterogeneous ontologies in their entirety may lead to inconsistencies or unintended inferences. In this paper we propose a set of guidelines for importing required terms from an external resource into a target ontology. We describe the guidelines, their implementation, present some examples of application, and outline future work and extensions

OntoCheck: verifying ontology naming conventions and metadata completeness in Protégé 4

BACKGROUND: Although policy providers have outlined minimal metadata guidelines and naming conventions, ontologies of today still display inter- and intra-ontology heterogeneities in class labelling schemes and metadata completeness. This fact is at least partially due to missing or inappropriate tools. Software support can ease this situation and contribute to overall ontology consistency and quality by helping to enforce such conventions. OBJECTIVE: We provide a plugin for the Protégé Ontology editor to allow for easy checks on compliance towards ontology naming conventions and metadata completeness, as well as curation in case of found violations. IMPLEMENTATION: In a requirement analysis, derived from a prior standardization approach carried out within the OBO Foundry, we investigate the needed capabilities for software tools to check, curate and maintain class naming conventions. A Protégé tab plugin was implemented accordingly using the Protégé 4.1 libraries. The plugin was tested on six different ontologies. Based on these test results, the plugin could be refined, also by the integration of new functionalities. RESULTS: The new Protégé plugin, OntoCheck, allows for ontology tests to be carried out on OWL ontologies. In particular the OntoCheck plugin helps to clean up an ontology with regard to lexical heterogeneity, i.e. enforcing naming conventions and metadata completeness, meeting most of the requirements outlined for such a tool. Found test violations can be corrected to foster consistency in entity naming and meta-annotation within an artefact. Once specified, check constraints like name patterns can be stored and exchanged for later re-use. Here we describe a first version of the software, illustrate its capabilities and use within running ontology development efforts and briefly outline improvements resulting from its application. Further, we discuss OntoChecks capabilities in the context of related tools and highlight potential future expansions. CONCLUSIONS: The OntoCheck plugin facilitates labelling error detection and curation, contributing to lexical quality assurance in OWL ontologies. Ultimately, we hope this Protégé extension will ease ontology alignments as well as lexical post-processing of annotated data and hence can increase overall secondary data usage by humans and computers

Chapter 11: Virtual Interviewers, Social Identities, and Survey Measurement Error. Appendix 11

Table A11A.1 Proportion of race-related items for which race of interviewer effects are observed across eleven published studies. Table A11A.2 Virtual interviewer assignments and linked example videos, N=1,735 Table A11A.3. Debriefing questionnaire about respondents’ experience administered textually after the primary date were collected Table A11A.4 Respondent – Virtual interviewer gender and race assignments, and match conditions N=1,735 Table A11A.5 Respondent characteristics, N=1,735 Table A11A.6 Questionnaire administered to respondents. Table A11A.7 Respondent gender and race choices, N=1,73

Survey-based naming conventions for use in OBO Foundry ontology development

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data

Analysis of Heating Effects and Deformations for a STAF Panel with a Coupled CFD and FEM Simulation Method

Conventional sandwich panels are one of the cheapest and easiest solutions for forming the thermal building envelope of industrial buildings. They are pre-fabricated façade elements, of which millions of square metres have been produced and mounted every year. There is great potential to reduce the consumption of fossil fuels and CO2 emissions through the solar thermal activation of such a sandwich panel. In the course of the research project ABS-Network SIAT 125, a Solar Thermal Activated Façade (STAF) panel was designed which is to be optimised both thermally and structurally. This study shows a first version of a so-called ‘one way coupled’ thermal and structural analysis of a conventional sandwich panel compared to the STAF panel. For this purpose, the numerical methods of Computational Fluid Dynamics (CFD) and Finite Element Method (FEM) are used  together in one simulation environment. Furthermore, results from an outdoor test facility are presented where a first version of a STAF panel is tested under real climate conditions. The CFD model was positively evaluated by comparing measured and computed temperatures

FAIR Computational Workflows

Computational workflows describe the complex multi-step methods that are used for data collection, data preparation, analytics, predictive modelling, and simulation that lead to new data products. They can inherently contribute to the FAIR data principles: by processing data according to established metadata; by creating metadata themselves during the processing of data; and by tracking and recording data provenance. These properties aid data quality assessment and contribute to secondary data usage. Moreover, workflows are digital objects in their own right. This paper argues that FAIR principles for workflows need to address their specific nature in terms of their composition of executable software steps, their provenance, and their development.Accepted for Data Intelligence special issue: FAIR best practices 2019. Carole Goble acknowledges funding by BioExcel2 (H2020 823830), IBISBA1.0 (H2020 730976) and EOSCLife (H2020 824087) . Daniel Schober's work was financed by Phenomenal (H2020 654241) at the initiation-phase of this effort, current work in kind contribution. Kristian Peters is funded by the German Network for Bioinformatics Infrastructure (de.NBI) and acknowledges BMBF funding under grant number 031L0107. Stian Soiland-Reyes is funded by BioExcel2 (H2020 823830). Daniel Garijo, Yolanda Gil, gratefully acknowledge support from DARPA award W911NF-18-1-0027, NIH award 1R01AG059874-01, and NSF award ICER-1740683