A quick guide for student-driven community genome annotation

High quality gene models are necessary to expand the molecular and genetic tools available for a target organism, but these are available for only a handful of model organisms that have undergone extensive curation and experimental validation over the course of many years. The majority of gene models present in biological databases today have been identified in draft genome assemblies using automated annotation pipelines that are frequently based on orthologs from distantly related model organisms. Manual curation is time consuming and often requires substantial expertise, but is instrumental in improving gene model structure and identification. Manual annotation may seem to be a daunting and cost-prohibitive task for small research communities but involving undergraduates in community genome annotation consortiums can be mutually beneficial for both education and improved genomic resources. We outline a workflow for efficient manual annotation driven by a team of primarily undergraduate annotators. This model can be scaled to large teams and includes quality control processes through incremental evaluation. Moreover, it gives students an opportunity to increase their understanding of genome biology and to participate in scientific research in collaboration with peers and senior researchers at multiple institutions

Context Aware Computing for The Internet of Things: A Survey

As we are moving towards the Internet of Things (IoT), the number of sensors deployed around the world is growing at a rapid pace. Market research has shown a significant growth of sensor deployments over the past decade and has predicted a significant increment of the growth rate in the future. These sensors continuously generate enormous amounts of data. However, in order to add value to raw sensor data we need to understand it. Collection, modelling, reasoning, and distribution of context in relation to sensor data plays critical role in this challenge. Context-aware computing has proven to be successful in understanding sensor data. In this paper, we survey context awareness from an IoT perspective. We present the necessary background by introducing the IoT paradigm and context-aware fundamentals at the beginning. Then we provide an in-depth analysis of context life cycle. We evaluate a subset of projects (50) which represent the majority of research and commercial solutions proposed in the field of context-aware computing conducted over the last decade (2001-2011) based on our own taxonomy. Finally, based on our evaluation, we highlight the lessons to be learnt from the past and some possible directions for future research. The survey addresses a broad range of techniques, methods, models, functionalities, systems, applications, and middleware solutions related to context awareness and IoT. Our goal is not only to analyse, compare and consolidate past research work but also to appreciate their findings and discuss their applicability towards the IoT.Comment: IEEE Communications Surveys & Tutorials Journal, 201

Toward a Standardized Strategy of Clinical Metabolomics for the Advancement of Precision Medicine

Despite the tremendous success, pitfalls have been observed in every step of a clinical metabolomics workflow, which impedes the internal validity of the study. Furthermore, the demand for logistics, instrumentations, and computational resources for metabolic phenotyping studies has far exceeded our expectations. In this conceptual review, we will cover inclusive barriers of a metabolomics-based clinical study and suggest potential solutions in the hope of enhancing study robustness, usability, and transferability. The importance of quality assurance and quality control procedures is discussed, followed by a practical rule containing five phases, including two additional "pre-pre-" and "post-post-" analytical steps. Besides, we will elucidate the potential involvement of machine learning and demonstrate that the need for automated data mining algorithms to improve the quality of future research is undeniable. Consequently, we propose a comprehensive metabolomics framework, along with an appropriate checklist refined from current guidelines and our previously published assessment, in the attempt to accurately translate achievements in metabolomics into clinical and epidemiological research. Furthermore, the integration of multifaceted multi-omics approaches with metabolomics as the pillar member is in urgent need. When combining with other social or nutritional factors, we can gather complete omics profiles for a particular disease. Our discussion reflects the current obstacles and potential solutions toward the progressing trend of utilizing metabolomics in clinical research to create the next-generation healthcare system.11Ysciescopu

Statistical parsing of morphologically rich languages (SPMRL): what, how and whither

The term Morphologically Rich Languages (MRLs) refers to languages in which significant information concerning syntactic units and relations is expressed at word-level. There is ample evidence that the application of readily available statistical parsing models to such languages is susceptible to serious performance degradation. The first workshop on statistical parsing of MRLs hosts a variety of contributions which show that despite language-specific idiosyncrasies, the problems associated with parsing MRLs cut across languages and parsing frameworks. In this paper we review the current state-of-affairs with respect to parsing MRLs and point out central challenges. We synthesize the contributions of researchers working on parsing Arabic, Basque, French, German, Hebrew, Hindi and Korean to point out shared solutions across languages. The overarching analysis suggests itself as a source of directions for future investigations

Advanced Knowledge Technologies at the Midterm: Tools and Methods for the Semantic Web

The University of Edinburgh and research sponsors are authorised to reproduce and distribute reprints and on-line copies for their purposes notwithstanding any copyright annotation hereon. The views and conclusions contained herein are the author’s and shouldn’t be interpreted as necessarily representing the official policies or endorsements, either expressed or implied, of other parties.In a celebrated essay on the new electronic media, Marshall McLuhan wrote in 1962:Our private senses are not closed systems but are endlessly translated into each other in that experience which we call consciousness. Our extended senses, tools, technologies, through the ages, have been closed systems incapable of interplay or collective awareness. Now, in the electric age, the very instantaneous nature of co-existence among our technological instruments has created a crisis quite new in human history. Our extended faculties and senses now constitute a single field of experience which demands that they become collectively conscious. Our technologies, like our private senses, now demand an interplay and ratio that makes rational co-existence possible. As long as our technologies were as slow as the wheel or the alphabet or money, the fact that they were separate, closed systems was socially and psychically supportable. This is not true now when sight and sound and movement are simultaneous and global in extent. (McLuhan 1962, p.5, emphasis in original)Over forty years later, the seamless interplay that McLuhan demanded between our technologies is still barely visible. McLuhan’s predictions of the spread, and increased importance, of electronic media have of course been borne out, and the worlds of business, science and knowledge storage and transfer have been revolutionised. Yet the integration of electronic systems as open systems remains in its infancy.Advanced Knowledge Technologies (AKT) aims to address this problem, to create a view of knowledge and its management across its lifecycle, to research and create the services and technologies that such unification will require. Half way through its sixyear span, the results are beginning to come through, and this paper will explore some of the services, technologies and methodologies that have been developed. We hope to give a sense in this paper of the potential for the next three years, to discuss the insights and lessons learnt in the first phase of the project, to articulate the challenges and issues that remain.The WWW provided the original context that made the AKT approach to knowledge management (KM) possible. AKT was initially proposed in 1999, it brought together an interdisciplinary consortium with the technological breadth and complementarity to create the conditions for a unified approach to knowledge across its lifecycle. The combination of this expertise, and the time and space afforded the consortium by the IRC structure, suggested the opportunity for a concerted effort to develop an approach to advanced knowledge technologies, based on the WWW as a basic infrastructure.The technological context of AKT altered for the better in the short period between the development of the proposal and the beginning of the project itself with the development of the semantic web (SW), which foresaw much more intelligent manipulation and querying of knowledge. The opportunities that the SW provided for e.g., more intelligent retrieval, put AKT in the centre of information technology innovation and knowledge management services; the AKT skill set would clearly be central for the exploitation of those opportunities.The SW, as an extension of the WWW, provides an interesting set of constraints to the knowledge management services AKT tries to provide. As a medium for the semantically-informed coordination of information, it has suggested a number of ways in which the objectives of AKT can be achieved, most obviously through the provision of knowledge management services delivered over the web as opposed to the creation and provision of technologies to manage knowledge.AKT is working on the assumption that many web services will be developed and provided for users. The KM problem in the near future will be one of deciding which services are needed and of coordinating them. Many of these services will be largely or entirely legacies of the WWW, and so the capabilities of the services will vary. As well as providing useful KM services in their own right, AKT will be aiming to exploit this opportunity, by reasoning over services, brokering between them, and providing essential meta-services for SW knowledge service management.Ontologies will be a crucial tool for the SW. The AKT consortium brings a lot of expertise on ontologies together, and ontologies were always going to be a key part of the strategy. All kinds of knowledge sharing and transfer activities will be mediated by ontologies, and ontology management will be an important enabling task. Different applications will need to cope with inconsistent ontologies, or with the problems that will follow the automatic creation of ontologies (e.g. merging of pre-existing ontologies to create a third). Ontology mapping, and the elimination of conflicts of reference, will be important tasks. All of these issues are discussed along with our proposed technologies.Similarly, specifications of tasks will be used for the deployment of knowledge services over the SW, but in general it cannot be expected that in the medium term there will be standards for task (or service) specifications. The brokering metaservices that are envisaged will have to deal with this heterogeneity.The emerging picture of the SW is one of great opportunity but it will not be a wellordered, certain or consistent environment. It will comprise many repositories of legacy data, outdated and inconsistent stores, and requirements for common understandings across divergent formalisms. There is clearly a role for standards to play to bring much of this context together; AKT is playing a significant role in these efforts. But standards take time to emerge, they take political power to enforce, and they have been known to stifle innovation (in the short term). AKT is keen to understand the balance between principled inference and statistical processing of web content. Logical inference on the Web is tough. Complex queries using traditional AI inference methods bring most distributed computer systems to their knees. Do we set up semantically well-behaved areas of the Web? Is any part of the Web in which semantic hygiene prevails interesting enough to reason in? These and many other questions need to be addressed if we are to provide effective knowledge technologies for our content on the web