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Conceptual Model-based Systems Biology: mapping knowledge and discovering gaps in the mRNA transcription cycle.

ABSTRACT: We propose a Conceptual Model-based Systems Biology framework for qualitative modeling, executing, and eliciting knowledge gaps in molecular biology systems. The framework is an adaptation of Object-Process Methodology (OPM), a graphical and textual executable modeling language. OPM enables concurrent representation of the system's structure-the objects that comprise the system, and behavior-how processes transform objects over time. Applying a top-down approach of recursively zooming into processes, we model a case in point-the mRNA transcription cycle. Starting with this high level cell function, we model increasingly detailed processes along with participating objects. Our modeling approach is capable of modeling molecular processes such as complex formation, localization and trafficking, molecular binding, enzymatic stimulation, and environmental intervention. At the lowest level, similar to the Gene Ontology, all biological processes boil down to three basic molecular functions: catalysis, binding/dissociation, and transporting. During modeling and execution of the mRNA transcription model, we discovered knowledge gaps, which we present and classify into various types. We also show how model execution enhances a coherent model construction. Identification and pinpointing knowledge gaps is an important feature of the framework, as it suggests where research should focus and whether conjectures about uncertain mechanisms fit into the already verified model.

SUBMITTER: Somekh J

PROVIDER: S-EPMC3536069 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:A valuable strategy to support conservation planning is to assess knowledge gaps regarding primary species occurrence data to identify and select areas for future biodiversity surveys. Currently, increasing accessibility to these data allows a cost-effective method for boosting knowledge about a country's biodiversity. For understudied countries where the lack of resources for conservation is more pronounced to resort to primary biodiversity data can be especially beneficial. Here, using a primary species occurrence dataset, we assessed and mapped Mozambique's knowledge gaps regarding terrestrial mammal species by identifying areas that are geographically distant and environmentally different from well-known sites. By comparing gaps from old and recent primary species occurrence data, we identified: (i) gaps of knowledge over time, (ii) the lesser-known taxa, and (iii) areas with potential for spatiotemporal studies. Our results show that the inventory of Mozambique's mammal fauna is near-complete in less than 5% of the territory, with broad areas of the country poorly sampled or not sampled at all. The knowledge gap areas are mostly associated with two ecoregions. The provinces lacking documentation coincide with areas over-explored for natural resources, and many such sites may never be documented. It is our understanding that by prioritising the survey of the knowledge-gap areas will likely produce new records for the country and, continuing the study of the well-known regions will guarantee their potential use for spatiotemporal studies. The implemented approach to assess the knowledge gaps from primary species occurrence data proved to be a powerful strategy to generate information that is essential to species conservation and management plan. However, we are aware that the impact of digital and openly available data depends mostly on its completeness and accuracy, and thus we encourage action from the scientific community and government authorities to support and promote data mobilisation.

Project description:BackgroundTo summarize global research trends and activities on multimorbidity; then to assess the knowledge gaps and to identify implications for knowledge exchange between high income countries (HICs) and low- and middle- income countries (LMICs).MethodsA comprehensive search was conducted to identify research publications on multimorbidity in the Web of ScienceTM, as well as diabetes, depression, hypertension, and Chronic Obstructive Pulmonary Disease (COPD). The time frame for the search was from 1900 to June, 2016. Information (such as publication date, subject category, author, country of origin, title, abstract, and keywords) were extracted and the full texts were obtained for the co-citation analysis. Data were linked with the life expectancy at birth (years) and Gross National Income (GNI). Co-citation and hierarchal clustering analysis was used to map the trends and research networks with CiteSpace II (JAVA freeware, copyright Chaomei Chen, http://cluster.cis.drexel.edu/~cchen/citespace/).FindingsWe identified 2864 relevant publications as at June 2016, with the first paper on this topic indexed in 1974 from Germany, but 80% were published after 2010. Further analysis yielded two knowledge gaps: (1) compared with single conditions (diabetes, hypertension, depression, and COPD), there is a mismatch between the high prevalence of multimorbidity and its research outputs (ratio of articles on multimorbidity vs other four single conditions is 1:13-150); (2) although a total of 76 countries have contributed to this research area, only 5% of research originated from LMICs where 73% of non-communicable disease (NCD) related deaths had occurred. Additional analysis showed the median year of first publication occurred 15 years later in the LMICs compared with HICs (2010 vs 1995); and longer life expectancy was associated with exponentially higher publication outputs (Pearson correlation coefficient r?=?0.95) at the global level. The life expectancy at the median year (1994) of first publication was 66.1, with the gap between LMICs and HICs 7.9 (68.4 vs 76.3).ConclusionsThis study confirms substantial knowledge gaps in the research agenda on multimorbidity, with input urgently needed to move us forward worldwide, especially for and in LMICs. There is the possibility that LMICs can learn from and collaborate with HICs in this area.

Project description:Background: Forensic psychiatric care treats mentally disordered offenders who suffer mainly from psychotic disorders, although comorbidities such as personality disorders, neurodevelopmental disorders, and substance abuse are common. A large proportion of these patients have committed violent crimes. Their care is involuntary, and their caregivers' mission is complex: not only to rehabilitate the patient, but also to consider their risk for reoffending and their risk to society. The objective of this overview of systematic reviews is to identify, appraise, and summarize the existing knowledge in forensic psychiatric care and identify knowledge gaps that require further research. Methods: We undertook a systematic literature search for systematic reviews in five defined domains considered important in daily clinical practice within the forensic psychiatric care: (1) diagnostic assessment and risk assessments; (2) pharmacological treatment; (3) psychological interventions; (4) psychosocial interventions, rehabilitation, and habilitation; and (5) restraint interventions. The target population was mentally disordered offenders (forensic psychiatric patients aged >15 years). Each abstract and full text review was assessed by two of the authors. Relevant reviews then were assessed for bias, and those with moderate or low risk of bias were included. Results: Of 38 systematic reviews meeting the inclusion criteria, only four had a moderate risk of bias. Two aimed to incorporate as many aspects of forensic psychiatric care as possible, one investigated non-pharmacological interventions to reduce aggression in forensic psychiatric care, and one focused on women with intellectual disabilities in forensic care. However, most of the primary studies included in these reviews had high risks of bias, and therefore, no conclusions could be drawn. All of our identified domains must be considered knowledge gaps. Conclusion: We could not answer any of our research questions within the five domains because of the high risk of bias in the primary studies in the included systematic reviews. There is an urgent need for more research on forensic psychiatric care since all of our studied domains were considered knowledge gaps.

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Conceptual Model-based Systems Biology: mapping knowledge and discovering gaps in the mRNA transcription cycle.

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