Towards Interoperability in Genome Databases: The MAtDB (MIPS Arabidopsis Thaliana Database) Experience

Increasing numbers of whole-genome sequences are available, but to interpret them fully requires more than listing all genes. Genome databases are faced with the challenges of integrating heterogenous data and enabling data mining. In comparison to a data warehousing approach, where integration is achieved through replication of all relevant data in a unified schema, distributed approaches provide greater flexibility and maintainability. These are important in a field where new data is generated rapidly and our understanding of the data changes. Interoperability between distributed data sources allows data maintenance to be separated from integration and analysis. Simple ways to access the data can facilitate the development of new data mining tools and the transition from model genome analysis to comparative genomics. With the MIPS Arabidopsis thaliana genome database (MAtDB, http://mips.gsf.de/proj/thal/db) our aim is to go beyond a data repository towards creating an integrated knowledge resource. To this end, the Arabidopsis genome has been a backbone against which to structure and integrate heterogenous data. The challenges to be met are continuous updating of data, the design of flexible data models that can evolve with new data, the integration of heterogenous data, e.g. through the use of ontologies, comprehensive views and visualization of complex information, simple interfaces for application access locally or via the Internet, and knowledge transfer across species.     

Biobanks for genomics and genomics for biobanks

Biobanks include biological samples and attached databases. Human biobanks occur in research, technological development and medical activities. Population genomics is highly dependent on the availability of large biobanks. Ethical issues must be considered: protecting the rights of those people whose samples or data are in biobanks (information, autonomy, confidentiality, protection of private life), assuring the non-commercial use of human body elements and the optimal use of samples and data. They balance other issues, such as protecting the rights of researchers and companies, allowing long-term use of biobanks while detailed information on future uses is not available. At the level of populations, the traditional form of informed consent is challenged. Other dimensions relate to the rights of a group as such, in addition to individual rights. Conditions of return of results and/or benefit to a population need to be defined. With 'large-scale biobanking' a marked trend in genomics, new societal dimensions appear, regarding communication, debate, regulation, societal control and valorization of such large biobanks. Exploring how genomics can help health sector biobanks to become more rationally constituted and exploited is an interesting perspective. For example, evaluating how genomic approaches can help in optimizing haematopoietic stem cell donor registries using new markers and high-throughput techniques to increase immunogenetic variability in such registries is a challenge currently being addressed. Ethical issues in such contexts are important, as not only individual decisions or projects are concerned, but also national policies in the international arena and organization of democratic debate about science, medicine and society.     

Human embryonic stem cell registries: value, challenges and opportunities

The accelerating pace of human embryonic stem cell (hESC) research has created an urgent need for the development of hESC registries, information repositories intended to gather, organize and disseminate hESC information. Although of enormous value to this evolving field, registries face significant challenges to their development. These challenges include addressing the legal and ethical issues surrounding hESC derivation as well as complex intellectual property concerns. In addition to these issues, registries must develop tools to efficiently gather, validate and present many different types of hESC information from a variety of sources. Given the pace and regulatory complexities of this field, it is important that registries develop cooperative mechanisms to avoid duplication and more efficiently support hESC research.     

Integrating specimen databases and revisionary systematics

Arguments are presented for the merit of integrating specimen databases into the practice of revisionary systematics. Work flows, data connections, data outputs, and data standardization are enumerated as critical aspects of such integration. Background information is provided on the use of "barcodes" as unique specimen identifiers and on methods for efficient data capture. Examples are provided on how to achieve efficient workflows and data standardization, as well as data outputs and data integration.     

The Protein Data Bank and lessons in data management

The Protein Data Bank (PDB) is a widely used biological databaseof macromolecular structures with a long history. This historyis treated as lessons learned and is used to highlight whatare believed to be the best practices important to developersof biological databases today. While the focus is on data quality,data representation and the information technology to supportthese data, the non-data and technology issues cannot be ignored.The role of the human factor in the form of users, collaborators,scientific society and ad hoc committees is also included.      

Argudas: lessons for argumentation in biology based on a gene expression use case

BACKGROUND: In situ hybridisation gene expression information helps biologists identify where a gene is expressed. However, the databases that republish the experimental information online are often both incomplete and inconsistent. Non-monotonic reasoning can help resolve such difficulties - one such form of reasoning is computational argumentation. Essentially this involves asking a computer to debate (i.e. reason about) the validity of a particular statement. Arguments are produced for both sides - the statement is true and, the statement is false - then the most powerful argument is used. In this work the computer is asked to debate whether or not a gene is expressed in a particular mouse anatomical structure. The information generated during the debate can be passed to the biological end-user, enabling their own decision-making process. RESULTS: This paper examines the evolution of a system, Argudas, which tests using computational argumentation in an in situ gene hybridisation gene expression use case. Argudas reasons using information extracted from several different online resources that publish gene expression information for the mouse. The development and evaluation of two prototypes is discussed. Throughout a number of issues shall be raised including the appropriateness of computational argumentation in biology and the challenges faced when integrating apparently similar online biological databases. CONCLUSIONS: From the work described in this paper it is clear that for argumentation to be effective in the biological domain the argumentation community need to develop further the tools and resources they provide. Additionally, the biological community must tackle the incongruity between overlapping and adjacent resources, thus facilitating the integration and modelling of biological information. Finally, this work highlights both the importance of, and difficulty in creating, a good model of the domain.     

Impacts of nutritional technology on feeds offered to horses: A review of effects of processing on voluntary intake,digesta characteristics and feed utilisation

Advances in feed processing technology applied to diet systems for ruminant livestock have been used extensively in the equine feed industry. The translation of these technologies is an important area of interest for the feed processing industry servicing the various sectors of the equine industry such as feeds for the racing, meat, milk and urine production, as well as supplements for leisure horse use. However, there are few reviews examining impacts of feed processing technologies on the processes controlling voluntary intake or utilisation of processed feeds by horses. In this paper, some of the specific features of feeds and impacts of feed processing on factors controlling meal pattern, frequency and size, and digestive physiology will be addressed. Three main areas are examined in this review, being impacts of feed processing on processes of “information gathering” (sensory and nutritional knowledge) by the horse, eating behaviour of the horse offered processed feeds (notably issues of preference and control of short-term ingestion rate), and implications of constraints of digestive physiology, process and function on voluntary intake and digestibility of processed feeds. The review highlights areas of future research and development for nutritional technology to increase knowledge of interactions between equine physiology and feed processing to enhance efficiency of capture of nutrients and maintain the welfare of horses managed in the housed environment.     

Addressing the problems with life-science databases for traditional uses and systems biology

A prerequisite to systems biology is the integration of heterogeneous experimental data, which are stored in numerous life-science databases. However, a wide range of obstacles that relate to access, handling and integration impede the efficient use of the contents of these databases. Addressing these issues will not only be essential for progress in systems biology, it will also be crucial for sustaining the more traditional uses of life-science databases.     

The semantic metadatabase (SEMEDA): ontology based integration of federated molecular biological data sources

A system for "intelligent" semantic integration and querying of federated databases is being implemented by using three main components: A component which enables SQL access to integrated databases by database federation (MARGBench), an ontology based semantic metadatabase (SEMEDA) and an ontology based query interface (SEMEDA-query). In this publication we explain and demonstrate the principles, architecture and the use of SEMEDA. Since SEMEDA is implemented as 3 tiered web application database providers can enter all relevant semantic and technical information about their databases by themselves via a web browser. SEMEDA' s collaborative ontology editing feature is not restricted to database integration, and might also be useful for ongoing ontology developments, such as the "Gene Ontology" [2]. SEMEDA can be found at http://www-bm.cs.uni-magdeburg.de/semeda/. We explain how this ontologically structured information can be used for semantic database integration. In addition, requirements to ontologies for molecular biological database integration are discussed and relevant existing ontologies are evaluated. We further discuss how ontologies and structured knowledge sources can be used in SEMEDA and whether they can be merged supplemented or updated to meet the requirements for semantic database integration.     

Information Integration in Molecular Bioscience

Integrating information in the molecular biosciences involves more than the cross-referencing of sequences or structures. Experimental protocols, results of computational analyses, annotations and links to relevant literature form integral parts of this information, and impart meaning to sequence or structure. In this review, we examine some existing approaches to integrating information in the molecular biosciences. We consider not only technical issues concerning the integration of heterogeneous data sources and the corresponding semantic implications, but also the integration of analytical results. Within the broad range of strategies for integration of data and information, we distinguish between platforms and developments. We discuss two current platforms and six current developments, and identify what we believe to be their strengths and limitations. We identify key unsolved problems in integrating information in the molecular biosciences, and discuss possible strategies for addressing them including semantic integration using ontologies, XML as a data model, and graphical user interfaces as integrative environments.     

Assessing Youth Perceptions and Knowledge of Ethics at 4-H Horse Shows in Louisiana

Due to the increased awareness of animal welfare issues and sensitized attitudes throughout society, youth animal projects provide a unique opportunity to assess and impact youth understanding and attitudes regarding animal welfare. Animal ethics training is not an uncommon requirement for participants in 4-H livestock programs. However, participants in 4-H horse projects are not universally held to the same standard. The purpose of this study was to assess youth knowledge, attitudes, and confidence in understanding of equine welfare at the 4-H state horse show, as well as to determine the beliefs and observations of unethical practices, and if differences exist between those parameters in youth competitors. The results suggest that 4-H competitors are interested in ethics and believe that unethical behavior rarely occurs within the state 4-H horse project. However, youth report observing common unethical behaviors at the show, suggesting a disconnect between what they believe is unethical and what they actually observe. Educational opportunities exist within these animal projects and should be enhanced to address the gap in understanding.     

Intelligent infrastructure for sustainable potable water: a roundtable for emerging transnational research and technology development needs

PROBLEM STATEMENT: Recent commercial and residential development have substantially impacted the fluxes and quality of water that recharge the aquifers and discharges to streams, lakes and wetlands and, ultimately, is recycled for potable use. Whereas the contaminant sources may be varied in scope and composition, these issues of urban water sustainability are of public health concern at all levels of economic development worldwide, and require cheap and innovative environmental sensing capabilities and interactive monitoring networks, as well as tailored distributed water treatment technologies. To address this need, a roundtable was organized to explore the potential role of advances in biotechnology and bioengineering to aid in developing causative relationships between spatial and temporal changes in urbanization patterns and groundwater and surface water quality parameters, and to address aspects of socioeconomic constraints in implementing sustainable exploitation of water resources. WORKSHOP OUTCOMES: An interactive framework for quantitative analysis of the coupling between human and natural systems requires integrating information derived from online and offline point measurements with Geographic Information Systems (GIS)-based remote sensing imagery analysis, groundwater-surface water hydrologic fluxes and water quality data to assess the vulnerability of potable water supplies. Spatially referenced data to inform uncertainty-based dynamic models can be used to rank watershed-specific stressors and receptors to guide researchers and policymakers in the development of targeted sensing and monitoring technologies, as well as tailored control measures for risk mitigation of potable water from microbial and chemical environmental contamination. The enabling technologies encompass: (i) distributed sensing approaches for microbial and chemical contamination (e.g. pathogens, endocrine disruptors); (ii) distributed application-specific, and infrastructure-adaptive water treatment systems; (iii) geostatistical integration of monitoring data and GIS layers; and (iv) systems analysis of microbial and chemical proliferation in distribution systems. IMPACT: This operational framework is aimed at technology implementation while maximizing economic and public health benefits. The outcomes of the roundtable will further research agendas in information technology-based monitoring infrastructure development, integration of processes and spatial analysis, as well as in new educational and training platforms for students, practitioners and regulators. The potential for technology diffusion to emerging economies with limited financial resources is substantial.     

Critical role of bioinformatics in translating huge amounts of next-generation sequencing data into personalized medicine

Realizing personalized medicine requires integrating diverse data types with bioinformatics. The most vital data are genomic information for individuals that are from advanced next-generation sequencing (NGS) technologies at present. The technologies continue to advance in terms of both decreasing cost and sequencing speed with concomitant increase in the amount and complexity of the data. The prodigious data together with the requisite computational pipelines for data analysis and interpretation are stressors to IT infrastructure and the scientists conducting the work alike. Bioinformatics is increasingly becoming the rate-limiting step with numerous challenges to be overcome for translating NGS data for personalized medicine. We review some key bioinformatics tasks, issues, and challenges in contexts of IT requirements, data quality, analysis tools and pipelines, and validation of biomarkers.     

From Reductionism to Reintegration: Solving society’s most pressing problems requires building bridges between data types across the life sciences

Decades of reductionist approaches in biology have achieved spectacular progress, but the proliferation of subdisciplines, each with its own technical and social practices regarding data, impedes the growth of the multidisciplinary and interdisciplinary approaches now needed to address pressing societal challenges. Data integration is key to a reintegrated biology able to address global issues such as climate change, biodiversity loss, and sustainable ecosystem management. We identify major challenges to data integration and present a vision for a “Data as a Service”-oriented architecture to promote reuse of data for discovery. The proposed architecture includes standards development, new tools and services, and strategies for career-development and sustainability.

Data integration is key to the reintegration of biology and the pursuit of global issues such as climate change, biodiversity loss, and sustainable ecosystem management. This Essay defines the primary challenges in data integration and presents a vision for a "Data as a Service" (DaaS) oriented architecture that enables frictionless data reuse, hypothesis testing, and discovery.     

Integration,visualization and analysis of human interactome

Data integration and visualization are crucial to obtain meaningful hypotheses from the diversity of ‘omics’ fields and the large volume of heterogeneous and distributed data sets. In this review we focus on network analysis as a key technique to integrate, visualize and extrapolate relevant information from diverse data. We first describe challenges in integrating different types of data and then focus on systematically exploring network properties to gain insight into network function. We also describe the relationship between network structures and function of elements that form it. Next, we highlight the role of the interactome in connecting data derived from different experiments, and we stress the importance of network analysis to recognize interaction context-specific features. Finally, we present an example integration to demonstrate the value of the network approach in cancer research, and highlight the importance of dynamic data in the specific context of signaling pathways.     

生物多样性数据集成模式初探

本文以生物多样性研究发展现状的分析为基础,为生物多样性保护政策的制定提供可靠的数据支持为目标,通过对国内外几个著名的生物多样性数据库建设情况的分析,从相关学者的需求出发,提出了设计一个多层次多角度并带有一定人工智能的生物多样性集成数据库的构想。该系统基于都柏林核心(Dublin Core)的数据规范,并符合基于开放文献预研的元数据互操作协议(The Open Archixles Initiative Protocol for Metadata Hatvesting,OAIPMH)的标准,是一个集文字、图件、图片、声音、影像为一体的,能够在网上和硬件载体(如光盘)上同时进行发布的分布式数据库平台。其网上数据库系统的子系统之间以及子系统和硬件载体之间可以通过元数据获取的开放档案倡议协议互相交换数据。     

Sharing genomes: an integrated approach to funding, managing and distributing genomic clone resources

National biological resource centres have a vital role in archiving and distributing biological reagents that result from large-scale genome programmes. These reagents are invaluable to the research community as they enable independent validation of results disclosed in peer review and provide tools that facilitate the next steps in discovery science. Here we address the crucial issues of open access, quality of materials, integration with public databases and sustainability of resources.