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The hierarchy of evidence is a fundamental concept in evidence-based medicine, but existing models can be challenging to apply in laboratory-based health care disciplines, such as pathology, where the types of evidence and contexts are significantly different from interventional medicine. This project aimed to define a comprehensive and complementary framework of new levels of evidence for evaluating research in tumor pathology-introducing a novel Hierarchy of Research Evidence for Tumor Pathology collaboratively designed by pathologists with help from epidemiologists, public health professionals, oncologists, and scientists, specifically tailored for use by pathologists-and to aid in the production of the World Health Organization Classification of Tumors (WCT) evidence gap maps. To achieve this, we adopted a modified Delphi approach, encompassing iterative online surveys, expert oversight, and external peer review, to establish the criteria for evidence in tumor pathology, determine the optimal structure for the new hierarchy, and ascertain the levels of confidence for each type of evidence. Over a span of 4 months and 3 survey rounds, we collected 1104 survey responses, culminating in a 3-day hybrid meeting in 2023, where a new hierarchy was unanimously agreed upon. The hierarchy is organized into 5 research theme groupings closely aligned with the subheadings of the WCT, and it consists of 5 levels of evidence-level P1 representing evidence types that merit the greatest level of confidence and level P5 reflecting the greatest risk of bias. For the first time, an international collaboration of pathology experts, supported by the International Agency for Research on Cancer, has successfully united to establish a standardized approach for evaluating evidence in tumor pathology. We intend to implement this novel Hierarchy of Research Evidence for Tumor Pathology to map the available evidence, thereby enriching and informing the WCT effectively., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Background and Objectives: There is a growing concern for the transmission of arboviral infections by blood transfusion in Europe. However, no assessment of the risk of transmission through all European blood supplies has been reported. Risk regulations at a European level should take differences in local transmission risk and the risk of transmission by travelling donors into consideration., Materials and Methods: A risk model and publicly available tool were developed to calculate the risk of transmission by all European blood supplies for arboviral outbreaks within Europe. Data on individual European blood supplies from Council of Europe reports and inter-European travel data from EUROSTAT were used to populate this model., Results: Each neuroinvasive case of WNV reported in Europe will on average result in 0·43 (95%CI: 0·32-0·55) infected blood product by locally infected donors and 0·010 (95%CI: 0·006-0·015) infected products by travelling donors. On basis of the 1373 neuroinvasive human WNV cases reported in the outbreak of 2018, it is estimated that without safety interventions this outbreak would have resulted in 708 (95%CI: 523-922) infected components derived from resident donors. Noncompliance to European regulations, which requires donor deferral or testing of donors who visited WNV-infected areas, would have resulted in 7.4 (95%CI: 4·7-11·1) infected blood components derived from infectious travelling donors exposed in outbreak areas throughout Europe., Conclusion: The risk of WNV transmission by a local outbreak is on average 113 times (95%CI: 95-139), so two orders of magnitude higher than the risk of transmission by travelling donors in Europe., (© 2021 International Society of Blood Transfusion.)

Aims: The aim of this study is to explore the relationships of tricuspid annulus area (TAA) with right atrial maximal volume (RAVmax) and right ventricular end-diastolic volume (RVEDV) in healthy subjects and patients with functional tricuspid regurgitation (FTR) of different aetiologies and severities., Methods and Results: We enrolled 280 patients (median age 66 years, 59% women) with FTR due to left heart disease (LHD), pulmonary hypertension (PH), corrected tetralogy of Fallot (TOF), chronic atrial fibrillation (AF), and 210 healthy volunteers (45 years, 53% women). We measured TAA at mid-systole and end-diastole, tenting volume of tricuspid leaflets, RAVmax, and RVEDV by 3D echocardiography. Irrespective of TA measurement timing, TAA correlated more closely with RAVmax than with RVEDV in both controls and FTR patients. On multivariable analysis, RAVmax was the most important determinant of TAA, accounting for 41% (normals) and 56% (FTR) of TAA variance. In FTR patients, age, RVEDV, and left ventricular ejection fraction were also independently correlated with TAA. RAVmax (AUC = 0.81) and TAA (AUC = 0.78) had a greater ability than RVEDV (AUC = 0.72) to predict severe FTR (P < 0.05). Among FTR patients, those with AF had the largest RAVmax and smallest RVEDV. RAVmax and TA were significantly dilated in all FTR groups, except in TOF. PH and TOF had largest RVEDV, yet tenting volume was increased only in PH and LHD., Conclusion: RA volume is a major determinant of TAA, and RA enlargement is an important mechanism of TA dilation in FTR irrespective of cardiac rhythm and RV loading conditions., (Published on behalf of the European Society of Cardiology. All rights reserved. © The Author(s) 2020. For permissions, please email: journals.permissions@oup.com.)

Background: Olfactory receptors (ORs) constitute a large family of sensory proteins that enable us to recognize a wide range of chemical volatiles in the environment. By contrast to the extensive information about human olfactory thresholds for thousands of odorants, studies of the genetic influence on olfaction are limited to a few examples. To annotate on a broad scale the impact of mutations at the structural level, here we analyzed a compendium of 119,069 natural variants in human ORs collected from the public domain., Results: OR mutations were categorized depending on their genomic and protein contexts, as well as their frequency of occurrence in several human populations. Functional interpretation of the natural changes was estimated from the increasing knowledge of the structure and function of the G protein-coupled receptor (GPCR) family, to which ORs belong. Our analysis reveals an extraordinary diversity of natural variations in the olfactory gene repertoire between individuals and populations, with a significant number of changes occurring at the structurally conserved regions. A particular attention is paid to mutations in positions linked to the conserved GPCR activation mechanism that could imply phenotypic variation in the olfactory perception. An interactive web application (hORMdb, Human Olfactory Receptor Mutation Database) was developed for the management and visualization of this mutational dataset., Conclusion: We performed topological annotations and population analysis of natural variants of human olfactory receptors and provide an interactive application to explore human OR mutation data. We envisage that the utility of this information will increase as the amount of available pharmacological data for these receptors grow. This effort, together with ongoing research in the study of genetic changes in other sensory receptors could shape an emerging sensegenomics field of knowledge, which should be considered by food and cosmetic consumer product manufacturers for the benefit of the general population.

Aims: Quantitative echocardiography parameters are seldom used to grade tricuspid regurgitation (TR) severity due to relative paucity of validation studies and lack of prognostic data. To assess the relationship between TR severity and the composite endpoint of death and hospitalization for congestive heart failure (CHF); and to identify the threshold values of vena contracta width (VCavg), effective regurgitant orifice area (EROA), regurgitant volume (RegVol), and regurgitant fraction (RegFr) to define low, intermediate, and high-risk TR based on patients' outcome data., Methods and Results: A cohort of 296 patients with at least mild TR underwent 2D, 3D, and Doppler echocardiography. We built statistical models (adjusted for age, NYHA class, left ventricular ejection fraction, and pulmonary artery systolic pressure) for VCavg, EROA, RegVol, and RegFr to study their relationships with the hazard of outcome. The tertiles of the derived hazard values defined the threshold values of the quantitative parameters for TR severity grading. During 47-month follow-up, 32 deaths and 72 CHF occurred. Event-free rate was 14%, 48%, and 93% in patients with severe, moderate, and mild TR, respectively. Severe TR was graded as VCavg > 6 mm, EROA > 0.30 cm2, RegVol > 30 mL, and RegF > 45%., Conclusion: This outcome study demonstrates the prognostic value of quantitative parameters of TR severity and provides prognostically meaningful threshold values to grade TR severity in low, intermediate, and high risk., (Published on behalf of the European Society of Cardiology. All rights reserved. © The Author(s) 2020. For permissions, please email: journals.permissions@oup.com.)

In patients with structurally normal atrioventricular valvular apparatus, functional regurgitation of the mitral or tricuspid valves has been attributed mainly to ventricular dilation and/or dysfunction, through a combination of annulus dilation and tethering of the valve leaflets. The occurrence of functional regurgitation of atrioventricular valves in patients with long-standing persistent atrial fibrillation and atrial dilation but normal ventricular size and function has received much less attention, and its peculiar mechanisms still remain to be understood. This distinct form of functional regurgitation (i.e., "atrial functional regurgitation") may require different treatment and interventional repair approaches than the classical functional regurgitation due to ventricular dilatation and dysfunction ("ventricular functional regurgitation"), and current guideline recommendations do not yet address this distinction. Clarifying the differences in the pathophysiology of atrial functional regurgitation and its management implications is of paramount importance. This review describes briefly the comparative anatomy of mitral and tricuspid apparatus and the pathophysiology and typical echocardiographic features of atrial functional regurgitation compared with ventricular functional regurgitation, as well as the added value of three-dimensional echocardiography as an essential imaging tool to clarify the mechanisms involved in its development., (Copyright © 2019 American Society of Echocardiography. Published by Elsevier Inc. All rights reserved.)

Three-dimensional echocardiography (3DE) represents one of the most innovative advances in cardiovascular imaging over the last 20 years. Recent technological developments have fueled the full implementation of 3DE in clinical practice and expanded its impact on patient diagnosis, management, and prognosis. One of the most important clinical applications of transthoracic 3DE has been the quantitation of cardiac chamber volumes and function. The main limitations affecting two-dimensional echocardiography calculations of chamber volumes (i.e. geometric assumptions about cardiac chamber shape and view foreshortening) are overcome by 3DE that allows an actual measurement of their volumes. Transesophageal 3DE has been applied mainly to assess the anatomy and function of heart valves, congenital defects and masses in the beating heart. As reparative cardiac surgery and transcatheter procedures have become more and more popular to treat structural heart disease, transesophageal 3DE has become not only one of the main imaging modalities for procedure planning but also for intra-procedural guidance and assessment of procedural results. New image rendering modalities such as 3D printing, holographic display, and fusion of 3DE images with other radiological or nuclear modalities will further expand the clinical applications and indications of 3DE.

Introduction : Quantification of left ventricular (LV) size and function represents the most frequent indication for an echocardiographic study. New echocardiographic techniques have been developed over the last decades in an attempt to provide a more comprehensive, accurate, and reproducible assessment of LV function. Areas covered : Although two-dimensional echocardiography (2DE) is the recommended imaging modality to evaluate the LV, three-dimensional echocardiography (3DE) has proven to be more accurate, by avoiding geometric assumptions about LV geometry, and to have incremental value for outcome prediction in comparison to conventional 2DE. LV shape (sphericity) and mass are actually measured with 3DE. Myocardial deformation analysis using 3DE can early detect subclinical LV dysfunction, before any detectable change in LV ejection fraction. Expert opinion : 3DE eliminates the errors associated with foreshortening and geometric assumptions inherent to 2DE and 3DE measurements approach very closely those obtained by CMR (the current reference modality), while maintaining the unique clinical advantage of a safe, highly cost/effective, portable imaging technique, available to the cardiologist at bedside to translate immediately the echocardiography findings into the clinical decision-making process.

Current guidelines recommend transthoracic echocardiography to assess patients with functional tricuspid regurgitation (FTR) because it provides information regarding the presence of structural abnormalities of the tricuspid valve (TV), allows measurement of tricuspid annulus diameter, and evaluates severity of FTR by integrating data obtained from 2D and Doppler echocardiography. Critical components of the noninvasive evaluation include information regarding TV anatomy, tricuspid regurgitation severity, right ventricular size and systolic function, and associated findings such as estimated pulmonary artery pressure. However, most of the parameters included in the current recommendations to assess FTR are derived from the experience and knowledge developed about the mitral valve and have been transferred from the left to the right side of the heart without accounting for differences in anatomy of the tricuspid and mitral apparatus or for differences in hemodynamic environment in which the TV operates compared to its left counterpart., (Copyright © 2019 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.)

Biopharmaceutical industry R&D, and indeed other life sciences R&D such as biomedical, environmental, agricultural and food production, is becoming increasingly data-driven and can significantly improve its efficiency and effectiveness by implementing the FAIR (findable, accessible, interoperable, reusable) guiding principles for scientific data management and stewardship. By so doing, the plethora of new and powerful analytical tools such as artificial intelligence and machine learning will be able, automatically and at scale, to access the data from which they learn, and on which they thrive. FAIR is a fundamental enabler for digital transformation., (Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Software Containers are changing the way scientists and researchers develop, deploy and exchange scientific software. They allow labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. However, containers and software packages should be produced under certain rules and standards in order to be reusable, compatible and easy to integrate into pipelines and analysis workflows. Here, we presented a set of recommendations developed by the BioContainers Community to produce standardized bioinformatics packages and containers. These recommendations provide practical guidelines to make bioinformatics software more discoverable, reusable and transparent.  They are aimed to guide developers, organisations, journals and funders to increase the quality and sustainability of research software., Competing Interests: No competing interests were disclosed.

Metabolomics, the youngest of the major omics technologies, is supported by an active community of researchers and infrastructure developers across Europe. To coordinate and focus efforts around infrastructure building for metabolomics within Europe, a workshop on the "Future of metabolomics in ELIXIR" was organised at Frankfurt Airport in Germany. This one-day strategic workshop involved representatives of ELIXIR Nodes, members of the PhenoMeNal consortium developing an e-infrastructure that supports workflow-based metabolomics analysis pipelines, and experts from the international metabolomics community. The workshop established metabolite identification as the critical area, where a maximal impact of computational metabolomics and data management on other fields could be achieved. In particular, the existing four ELIXIR Use Cases, where the metabolomics community - both industry and academia - would benefit most, and which could be exhaustively mapped onto the current five ELIXIR Platforms were discussed. This opinion article is a call for support for a new ELIXIR metabolomics Use Case, which aligns with and complements the existing and planned ELIXIR Platforms and Use Cases., Competing Interests: Competing interests: No competing interests were disclosed.

Motivation: BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters)., Availability and Implementation: The software is freely available at github.com/BioContainers/., Contact: yperez@ebi.ac.uk., (© The Author(s) 2017. Published by Oxford University Press.)

In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such databases depends on the discipline of data science and on the humble bricks and mortar that make integration possible; identifiers are a core component of this integration infrastructure. Drawing on our experience and on work by other groups, we outline 10 lessons we have learned about the identifier qualities and best practices that facilitate large-scale data integration. Specifically, we propose actions that identifier practitioners (database providers) should take in the design, provision and reuse of identifiers. We also outline the important considerations for those referencing identifiers in various circumstances, including by authors and data generators. While the importance and relevance of each lesson will vary by context, there is a need for increased awareness about how to avoid and manage common identifier problems, especially those related to persistence and web-accessibility/resolvability. We focus strongly on web-based identifiers in the life sciences; however, the principles are broadly relevant to other disciplines.

Most bioinformatics tools available today were not written by professional software developers, but by people that wanted to solve their own problems, using computational solutions and spending the minimum time and effort possible, since these were just the means to an end. Consequently, a vast number of software applications are currently available, hindering the task of identifying the utility and quality of each. At the same time, this situation has hindered regular adoption of these tools in clinical practice. Typically, they are not sufficiently developed to be used by most clinical researchers and practitioners. To address these issues, it is necessary to re-think how biomedical applications are built and adopt new strategies that ensure quality, efficiency, robustness, correctness and reusability of software components. We also need to engage end-users during the development process to ensure that applications fit their needs. In this review, we present a set of guidelines to support biomedical software development, with an explanation of how they can be implemented and what kind of open-source tools can be used for each specific topic., Competing Interests: Competing interests: No competing interests were disclosed.

Metrics for assessing adoption of good development practices are a useful way to ensure that software is sustainable, reusable and functional. Sustainability means that the software used today will be available - and continue to be improved and supported - in the future. We report here an initial set of metrics that measure good practices in software development. This initiative differs from previously developed efforts in being a community-driven grassroots approach where experts from different organisations propose good software practices that have reasonable potential to be adopted by the communities they represent. We not only focus our efforts on understanding and prioritising good practices, we assess their feasibility for implementation and publish them here., Competing Interests: No competing interests were disclosed.

In response to increases in ambient temperature (Ta), many animals increase total evaporative water loss (TEWL) through their skin and respiratory passages to maintain a constant body temperature, a response that compromises water balance. In birds, cutaneous water loss (CWL) accounts for approximately 65% of TEWL at thermoneutral temperatures. Although the proportion of TEWL accounted for by CWL decreases to only 25% at high Ta, the magnitude of CWL still increases, suggesting changes in the barrier function of the skin. The stratum corneum (SC) is composed of flat, dead cells called corneocytes embedded in a matrix of lipids, many of which arrange in layers called lamellae. The classes of lipids that comprise these lamellae, and their attendant physical properties, determine the rate of CWL. We measured CWL at 25, 30, 35, and 40 °C in House Sparrows (Passer domesticus) caught in the winter and summer, and in sparrows acclimated to warm and cold lab environments. We then used Fourier transform infrared spectroscopy to measure lipid-lipid and lipid-water interactions in the SC under different conditions of temperature and hydration, and correlated these results with lipid classes in the SC. As CWL increased at higher temperatures, the amount of gauche defects in lipid alkyl chains increased, indicating that lipid disorder is partially responsible for higher CWL at high temperatures. However, variation in CWL between groups could not be explained by the amount of gauche defects, and this remaining variation may be attributed to greater amounts of cerebrosides in birds with low CWL, as the sugar moieties of cerebrosides lie outside lipid lamellae and form strong hydrogen bonds with water molecules., (Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.)

Data sharing, integration and annotation are essential to ensure the reproducibility of the analysis and interpretation of the experimental findings. Often these activities are perceived as a role that bioinformaticians and computer scientists have to take with no or little input from the experimental biologist. On the contrary, biological researchers, being the producers and often the end users of such data, have a big role in enabling biological data integration. The quality and usefulness of data integration depend on the existence and adoption of standards, shared formats, and mechanisms that are suitable for biological researchers to submit and annotate the data, so it can be easily searchable, conveniently linked and consequently used for further biological analysis and discovery. Here, we provide background on what is data integration from a computational science point of view, how it has been applied to biological research, which key aspects contributed to its success and future directions.

With the increasingly rapid growth of data in life sciences we are witnessing a major transition in the way research is conducted, from hypothesis-driven studies to data-driven simulations of whole systems. Such approaches necessitate the use of large-scale computational resources and e-infrastructures, such as the European Grid Infrastructure (EGI). EGI, one of key the enablers of the digital European Research Area, is a federation of resource providers set up to deliver sustainable, integrated and secure computing services to European researchers and their international partners. Here we aim to provide the state of the art of Grid/Cloud computing in EU research as viewed from within the field of life sciences, focusing on key infrastructures and projects within the life sciences community. Rather than focusing purely on the technical aspects underlying the currently provided solutions, we outline the design aspects and key characteristics that can be identified across major research approaches. Overall, we aim to provide significant insights into the road ahead by establishing ever-strengthening connections between EGI as a whole and the life sciences community.

Summary: Rapid technological advances have led to an explosion of biomedical data in recent years. The pace of change has inspired new collaborative approaches for sharing materials and resources to help train life scientists both in the use of cutting-edge bioinformatics tools and databases and in how to analyse and interpret large datasets. A prototype platform for sharing such training resources was recently created by the Bioinformatics Training Network (BTN). Building on this work, we have created a centralized portal for sharing training materials and courses, including a catalogue of trainers and course organizers, and an announcement service for training events. For course organizers, the portal provides opportunities to promote their training events; for trainers, the portal offers an environment for sharing materials, for gaining visibility for their work and promoting their skills; for trainees, it offers a convenient one-stop shop for finding suitable training resources and identifying relevant training events and activities locally and worldwide., Availability and Implementation: http://mygoblet.org/training-portal., (© The Author 2014. Published by Oxford University Press.)

Summary: Signaling pathways provide essential information on complex regulatory processes within the cell. They are moreover widely used to interpret and integrate data from large-scale studies, such as expression or functional screens. We present KEGGViewer a BioJS component to visualize KEGG pathways and to allow their visual integration with functional data., Availability: KEGGViewer is an open-source tool freely available at the BioJS Registry. Instructions on how to use the tool are available at http://goo.gl/dVeWpg and the source code can be found at http://github.com/biojs/biojs and DOI: 10.5281/zenodo.7708.

Summary: Protein interaction networks have become an essential tool in large-scale data analysis, integration, and the visualization of high-throughput data in the context of complex cellular networks. Many individual databases are available that provide information on binary interactions of proteins and small molecules. Community efforts such as PSICQUIC aim to unify and standardize information emanating from these public databases. Here we introduce PsicquicGraph, an open-source, web-based visualization component for molecular interactions from PSIQUIC services., Availability: PsicquicGraph is freely available at the BioJS Registry for download and enhancement. Instructions on how to use the tool are available here http://goo.gl/kDaIgZ and the source code can be found at http://github.com/biojs/biojs and DOI: 10.5281/zenodo.7709.

wigExplorer is a BioJS component whose main purpose is to provide a platform for visualisation of wig-formatted data. Wig files are extensively used by genome browsers such as the UCSC Genome Browser. wigExplorer follows the BioJS standard specification, requiring a simple configuration and installation. wigExplorer provides an easy way to navigate the visible region of the canvas and allows interaction with other components via predefined events. Availability: http://github.com/biojs/biojs; http://dx.doi.org/ 10.5281/zenodo.8516.

Rationale: Omics sciences enable a systems-level perspective in characterizing cardiovascular biology. Integration of diverse proteomics data via a computational strategy will catalyze the assembly of contextualized knowledge, foster discoveries through multidisciplinary investigations, and minimize unnecessary redundancy in research efforts., Objective: The goal of this project is to develop a consolidated cardiac proteome knowledgebase with novel bioinformatics pipeline and Web portals, thereby serving as a new resource to advance cardiovascular biology and medicine., Methods and Results: We created Cardiac Organellar Protein Atlas Knowledgebase (COPaKB; www.HeartProteome.org), a centralized platform of high-quality cardiac proteomic data, bioinformatics tools, and relevant cardiovascular phenotypes. Currently, COPaKB features 8 organellar modules, comprising 4203 LC-MS/MS experiments from human, mouse, drosophila, and Caenorhabditis elegans, as well as expression images of 10,924 proteins in human myocardium. In addition, the Java-coded bioinformatics tools provided by COPaKB enable cardiovascular investigators in all disciplines to retrieve and analyze pertinent organellar protein properties of interest., Conclusions: COPaKB provides an innovative and interactive resource that connects research interests with the new biological discoveries in protein sciences. With an array of intuitive tools in this unified Web server, nonproteomics investigators can conveniently collaborate with proteomics specialists to dissect the molecular signatures of cardiovascular phenotypes.

The mountains of data thrusting from the new landscape of modern high-throughput biology are irrevocably changing biomedical research and creating a near-insatiable demand for training in data management and manipulation and data mining and analysis. Among life scientists, from clinicians to environmental researchers, a common theme is the need not just to use, and gain familiarity with, bioinformatics tools and resources but also to understand their underlying fundamental theoretical and practical concepts. Providing bioinformatics training to empower life scientists to handle and analyse their data efficiently, and progress their research, is a challenge across the globe. Delivering good training goes beyond traditional lectures and resource-centric demos, using interactivity, problem-solving exercises and cooperative learning to substantially enhance training quality and learning outcomes. In this context, this article discusses various pragmatic criteria for identifying training needs and learning objectives, for selecting suitable trainees and trainers, for developing and maintaining training skills and evaluating training quality. Adherence to these criteria may help not only to guide course organizers and trainers on the path towards bioinformatics training excellence but, importantly, also to improve the training experience for life scientists.

Summary: We present iAnn, an open source community-driven platform for dissemination of life science events, such as courses, conferences and workshops. iAnn allows automatic visualisation and integration of customised event reports. A central repository lies at the core of the platform: curators add submitted events, and these are subsequently accessed via web services. Thus, once an iAnn widget is incorporated into a website, it permanently shows timely relevant information as if it were native to the remote site. At the same time, announcements submitted to the repository are automatically disseminated to all portals that query the system. To facilitate the visualization of announcements, iAnn provides powerful filtering options and views, integrated in Google Maps and Google Calendar. All iAnn widgets are freely available., Availability: http://iann.pro/iannviewer, Contact: manuel.corpas@tgac.ac.uk.

The Proteomics Standard Initiative Common QUery InterfaCe (PSICQUIC) specification was created by the Human Proteome Organization Proteomics Standards Initiative (HUPO-PSI) to enable computational access to molecular-interaction data resources by means of a standard Web Service and query language. Currently providing >150 million binary interaction evidences from 28 servers globally, the PSICQUIC interface allows the concurrent search of multiple molecular-interaction information resources using a single query. Here, we present an extension of the PSICQUIC specification (version 1.3), which has been released to be compliant with the enhanced standards in molecular interactions. The new release also includes a new reference implementation of the PSICQUIC server available to the data providers. It offers augmented web service capabilities and improves the user experience. PSICQUIC has been running for almost 5 years, with a user base growing from only 4 data providers to 28 (April 2013) allowing access to 151 310 109 binary interactions. The power of this web service is shown in PSICQUIC View web application, an example of how to simultaneously query, browse and download results from the different PSICQUIC servers. This application is free and open to all users with no login requirement (http://www.ebi.ac.uk/Tools/webservices/psicquic/view/main.xhtml).

Workflows are useful to perform data analysis and integration in systems biology. Workflow management systems can help users create workflows without any previous knowledge in programming and web services. However the computational skills required to build such workflows are usually above the level most biological experimentalists are comfortable with. In this chapter we introduce workflow management systems that reuse existing workflows instead of creating them, making it easier for experimentalists to perform computational tasks.

Funding bodies are increasingly recognizing the need to provide graduates and researchers with access to short intensive courses in a variety of disciplines, in order both to improve the general skills base and to provide solid foundations on which researchers may build their careers. In response to the development of 'high-throughput biology', the need for training in the field of bioinformatics, in particular, is seeing a resurgence: it has been defined as a key priority by many Institutions and research programmes and is now an important component of many grant proposals. Nevertheless, when it comes to planning and preparing to meet such training needs, tension arises between the reward structures that predominate in the scientific community which compel individuals to publish or perish, and the time that must be devoted to the design, delivery and maintenance of high-quality training materials. Conversely, there is much relevant teaching material and training expertise available worldwide that, were it properly organized, could be exploited by anyone who needs to provide training or needs to set up a new course. To do this, however, the materials would have to be centralized in a database and clearly tagged in relation to target audiences, learning objectives, etc. Ideally, they would also be peer reviewed, and easily and efficiently accessible for downloading. Here, we present the Bioinformatics Training Network (BTN), a new enterprise that has been initiated to address these needs and review it, respectively, to similar initiatives and collections.

This article aims to introduce the nature of data integration to life scientists. Generally, the subject of data integration is not discussed outside the field of computational science and is not covered in any detail, or even neglected, when teaching/training trainees. End users (hereby defined as wet-lab trainees, clinicians, lab researchers) will mostly interact with bioinformatics resources and tools through web interfaces that mask the user from the data integration processes. However, the lack of formal training or acquaintance with even simple database concepts and terminology often results in a real obstacle to the full comprehension of the resources and tools the end users wish to access. Understanding how data integration works is fundamental to empowering trainees to see the limitations as well as the possibilities when exploring, retrieving, and analysing biological data from databases. Here we introduce a game-based learning activity for training/teaching the topic of data integration that trainers/educators can adopt and adapt for their classroom. In particular we provide an example using DAS (Distributed Annotation Systems) as a method for data integration.

A large number of diverse, complex, and distributed data resources are currently available in the Bioinformatics domain. The pace of discovery and the diversity of information means that centralised reference databases like UniProt and Ensembl cannot integrate all potentially relevant information sources. From a user perspective however, centralised access to all relevant information concerning a specific query is essential. The Distributed Annotation System (DAS) defines a communication protocol to exchange annotations on genomic and protein sequences; this standardisation enables clients to retrieve data from a myriad of sources, thus offering centralised access to end-users.We introduce MyDas, a web server that facilitates the publishing of biological annotations according to the DAS specification. It deals with the common functionality requirements of making data available, while also providing an extension mechanism in order to implement the specifics of data store interaction. MyDas allows the user to define where the required information is located along with its structure, and is then responsible for the communication protocol details.

IntAct is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. Two levels of curation are now available within the database, with both IMEx-level annotation and less detailed MIMIx-compatible entries currently supported. As from September 2011, IntAct contains approximately 275,000 curated binary interaction evidences from over 5000 publications. The IntAct website has been improved to enhance the search process and in particular the graphical display of the results. New data download formats are also available, which will facilitate the inclusion of IntAct's data in the Semantic Web. IntAct is an active contributor to the IMEx consortium (http://www.imexconsortium.org). IntAct source code and data are freely available at http://www.ebi.ac.uk/intact.

Motivation: Dasty3 is a highly interactive and extensible Web-based framework. It provides a rich Application Programming Interface upon which it is possible to develop specialized clients capable of retrieving information from DAS sources as well as from data providers not using the DAS protocol. Dasty3 provides significant improvements on previous Web-based frameworks and is implemented using the 1.6 DAS specification., Availability: Dasty3 is an open-source tool freely available at http://www.ebi.ac.uk/dasty/ under the terms of the GNU General public license. Source and documentation can be found at http://code.google.com/p/dasty/., Contact: hhe@ebi.ac.uk.

Background: Centralised resources such as GenBank and UniProt are perfect examples of the major international efforts that have been made to integrate and share biological information. However, additional data that adds value to these resources needs a simple and rapid route to public access. The Distributed Annotation System (DAS) provides an adequate environment to integrate genomic and proteomic information from multiple sources, making this information accessible to the community. DAS offers a way to distribute and access information but it does not provide domain experts with the mechanisms to participate in the curation process of the available biological entities and their annotations., Results: We designed and developed a Collaborative Annotation System for proteins called DAS Writeback. DAS writeback is a protocol extension of DAS to provide the functionalities of adding, editing and deleting annotations. We implemented this new specification as extensions of both a DAS server and a DAS client. The architecture was designed with the involvement of the DAS community and it was improved after performing usability experiments emulating a real annotation task., Conclusions: We demonstrate that DAS Writeback is effective, usable and will provide the appropriate environment for the creation and evolution of community protein annotation.

Background: The Distributed Annotation System (DAS) has proven to be a successful way to publish and share biological data. Although there are more than 750 active registered servers from around 50 organizations, setting up a DAS server comprises a fair amount of work, making it difficult for many research groups to share their biological annotations. Given the clear advantage that the generalized sharing of relevant biological data is for the research community it would be desirable to facilitate the sharing process., Results: Here we present easyDAS, a web-based system enabling anyone to publish biological annotations with just some clicks. The system, available at http://www.ebi.ac.uk/panda-srv/easydas is capable of reading different standard data file formats, process the data and create a new publicly available DAS source in a completely automated way. The created sources are hosted on the EBI systems and can take advantage of its high storage capacity and network connection, freeing the data provider from any network management work. easyDAS is an open source project under the GNU LGPL license., Conclusions: easyDAS is an automated DAS source creation system which can help many researchers in sharing their biological data, potentially increasing the amount of relevant biological data available to the scientific community.

The Distributed Annotation System (DAS) is a protocol for easy sharing and integration of biological annotations. In order to visualize feature annotations in a genomic context a client is required. Here we present myKaryoView, a simple light-weight DAS tool for visualization of genomic annotation. myKaryoView has been specifically configured to help analyse data derived from personal genomics, although it can also be used as a generic genome browser visualization. Several well-known data sources are provided to facilitate comparison of known genes and normal variation regions. The navigation experience is enhanced by simultaneous rendering of different levels of detail across chromosomes. A simple interface is provided to allow searches for any SNP, gene or chromosomal region. User-defined DAS data sources may also be added when querying the system. We demonstrate myKaryoView capabilities for adding user-defined sources with a set of genetic profiles of family-related individuals downloaded directly from 23andMe. myKaryoView is a web tool for visualization of genomic data specifically designed for direct-to-consumer genomic data that uses publicly available data distributed throughout the Internet. It does not require data to be held locally and it is capable of rendering any feature as long as it conforms to DAS specifications. Configuration and addition of sources to myKaryoView can be done through the interface. Here we show a proof of principle of myKaryoView's ability to display personal genomics data with 23andMe genome data sources. The tool is available at: http://mykaryoview.com.

Motivation: The advent of sequencing and structural genomics projects has provided a dramatic boost in the number of uncharacterized protein structures and sequences. Consequently, many computational tools have been developed to help elucidate protein function. However, such services are spread throughout the world, often with standalone web pages. Integration of these methods is needed and so far this has not been possible as there was no common vocabulary available that could be used as a standard language., Results: The Protein Feature Ontology has been developed to provide a structured controlled vocabulary for features on a protein sequence or structure and comprises approximately 100 positional terms, now integrated into the Sequence Ontology (SO) and 40 non-positional terms which describe features relating to the whole-protein sequence. In addition, post-translational modifications are described by using a pre-existing ontology, the Protein Modification Ontology (MOD). This ontology is being used to integrate over 150 distinct annotations provided by the BioSapiens Network of Excellence, a consortium comprising 19 partner sites in Europe., Availability: The Protein Feature Ontology can be browsed by accessing the ontology lookup service at the European Bioinformatics Institute (http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BS).

Background: Ontologies such as the Gene Ontology can enable the construction of complex queries over biological information in a conceptual way, however existing systems to do this are too technical. Within the biological domain there is an increasing need for software that facilitates the flexible retrieval of information. OntoDas aims to fulfil this need by allowing the definition of queries by selecting valid ontology terms., Results: OntoDas is a web-based tool that uses information visualisation techniques to provide an intuitive, interactive environment for constructing ontology-based queries against the Gene Ontology Database. Both a comprehensive use case and the interface itself were designed in a participatory manner by working with biologists to ensure that the interface matches the way biologists work. OntoDas was further tested with a separate group of biologists and refined based on their suggestions., Conclusion: OntoDas provides a visual and intuitive means for constructing complex queries against the Gene Ontology. It was designed with the participation of biologists and compares favourably with similar tools. It is available at http://ontodas.nbn.ac.za.

Summary: Dasty2 is a highly interactive web client integrating protein sequence annotations from currently more than 40 sources, using the distributed annotation system (DAS)., Availability: Dasty2 is an open source tool freely available under the terms of the Apache License 2.0, publicly available at http://www.ebi.ac.uk/dasty/.

Background: The Distributed Annotation System (DAS) is a widely adopted protocol for dynamically integrating a wide range of biological data from geographically diverse sources. DAS continues to expand its applicability and evolve in response to new challenges facing integrative bioinformatics., Results: Here we describe the various infrastructure components of DAS and present a new extended version of the DAS specification. Version 1.53E incorporates several recent developments, including its extension to serve new data types and an ontology for protein features., Conclusion: Our extensions to the DAS protocol have facilitated the integration of new data types, and our improvements to the existing DAS infrastructure have addressed recent challenges. The steadily increasing numbers of available data sources demonstrates further adoption of the DAS protocol.