EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats.

MOTIVATION: Advancing the search, publication and integration of bioinformatics tools and resources demands consistent machine-understandable descriptions. A comprehensive ontology allowing such descriptions is therefore required. RESULTS: EDAM is an ontology of bioinformatics operations (tool or workflow functions), types of data and identifiers, application domains and data formats. EDAM supports semantic annotation of diverse entities such as Web services, databases, programmatic libraries, standalone tools, interactive applications, data schemas, datasets and publications within bioinformatics. EDAM applies to organizing and finding suitable tools and data and to automating their integration into complex applications or workflows. It includes over 2200 defined concepts and has successfully been used for annotations and implementations. AVAILABILITY: The latest stable version of EDAM is available in OWL format from http://edamontology.org/EDAM.owl and in OBO format from http://edamontology.org/EDAM.obo. It can be viewed online at the NCBO BioPortal and the EBI Ontology Lookup Service. For documentation and license please refer to http://edamontology.org. This article describes version 1.2 available at http://edamontology.org/EDAM_1.2.owl. CONTACT: jison@ebi.ac.uk.

NucleaRDB: information system for nuclear receptors.

The NucleaRDB is a Molecular Class-Specific Information System that collects, combines, validates and disseminates large amounts of heterogeneous data on nuclear hormone receptors. It contains both experimental and computationally derived data. The data and knowledge present in the NucleaRDB can be accessed using a number of different interactive and programmatic methods and query systems. A nuclear hormone receptor-specific PDF reader interface is available that can integrate the contents of the NucleaRDB with full-text scientific articles. The NucleaRDB is freely available at http://www.receptors.org/nucleardb.

BioCatalogue: a universal catalogue of web services for the life sciences.

The use of Web Services to enable programmatic access to on-line bioinformatics is becoming increasingly important in the Life Sciences. However, their number, distribution and the variable quality of their documentation can make their discovery and subsequent use difficult. A Web Services registry with information on available services will help to bring together service providers and their users. The BioCatalogue (http://www.biocatalogue.org/) provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Services in the BioCatalogue can be described and searched in multiple ways based upon their technical types, bioinformatics categories, user tags, service providers or data inputs and outputs. They are also subject to constant monitoring, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. The system is accessible via a human-readable 'Web 2.0'-style interface and a programmatic Web Service interface. The BioCatalogue follows a community approach in which all services can be registered, browsed and incrementally documented with annotations by any member of the scientific community.

The EMBRACE web service collection.

The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web services for use in the life sciences. The project concluded that in order for web services to achieve widespread adoption, standards must be defined for the choice of web service technology, for semantically annotating both service function and the data exchanged, and a mechanism for discovering services must be provided. Building on this, the project developed: EDAM, an ontology for describing life science web services; BioXSD, a schema for exchanging data between services; and a centralized registry (http://www.embraceregistry.net) that collects together around 1000 services developed by the consortium partners. This article presents the current status of the collection and its associated recommendations and standards definitions.

Integrating GPCR-specific information with full text articles.

BACKGROUND: With the continued growth in the volume both of experimental G protein-coupled receptor (GPCR) data and of the related peer-reviewed literature, the ability of GPCR researchers to keep up-to-date is becoming increasingly curtailed. RESULTS: We present work that integrates the biological data and annotations in the GPCR information system (GPCRDB) with next-generation methods for intelligently exploring, visualising and interacting with the scientific articles used to disseminate them. This solution automatically retrieves relevant information from GPCRDB and displays it both within and as an adjunct to an article. CONCLUSIONS: This approach allows researchers to extract more knowledge more swiftly from literature. Importantly, it allows reinterpretation of data in articles published before GPCR structure data became widely available, thereby rescuing these valuable data from long-dormant sources.

BioXSD: the common data-exchange format for everyday bioinformatics web services.

MOTIVATION: The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more of the resources offer programmatic web-service interface. However, efficient use of the resources is hampered by the lack of widely used, standard data-exchange formats for the basic, everyday bioinformatics data types. RESULTS: BioXSD has been developed as a candidate for standard, canonical exchange format for basic bioinformatics data. BioXSD is represented by a dedicated XML Schema and defines syntax for biological sequences, sequence annotations, alignments and references to resources. We have adapted a set of web services to use BioXSD as the input and output format, and implemented a test-case workflow. This demonstrates that the approach is feasible and provides smooth interoperability. Semantics for BioXSD is provided by annotation with the EDAM ontology. We discuss in a separate section how BioXSD relates to other initiatives and approaches, including existing standards and the Semantic Web. AVAILABILITY: The BioXSD 1.0 XML Schema is freely available at http://www.bioxsd.org/BioXSD-1.0.xsd under the Creative Commons BY-ND 3.0 license. The http://bioxsd.org web page offers documentation, examples of data in BioXSD format, example workflows with source codes in common programming languages, an updated list of compatible web services and tools and a repository of feature requests from the community.

Views of Practitioners and Researchers on the Use of Virtual Reality in Treatments for Substance Use Disorders.

Virtual Reality Therapy (VRT) has been shown to be effective in treating anxiety disorders and phobias, but has not yet been widely tested for Substance Use Disorders (SUDs) and it is not known whether health care practitioners working with SUDs would use VRT if it were available. We report the results of an interview study exploring practitioners' and researchers' views on the utility of VRT for SUD treatment. Practitioners and researchers with at least two years' experience delivering or researching and designing SUD treatments were recruited (n = 14). Interviews were thematically analyzed, resulting in themes relating to the safety and realism of VRT, and the opportunity for the additional insight it could offer to during SUD treatment. Participants were positive about employing VRT as an additional treatment for SUD. VRT was thought suitable for treating adults and people with mental health issues or trauma, provided that risks were appropriately managed. Subsequent relapse, trauma and over-confidence in the success of treatment were identified as risks. The opportunity VRT offered to include other actors in therapy (via avatar use), and observe reactions, were benefits that could not currently be achieved with other forms of therapy. Overall, VRT was thought to offer the potential for safe, realistic, personalized and insightful exposure to diverse triggering scenarios, and to be acceptable for integration into a wide range of SUD treatments.

Experience using web services for biological sequence analysis.

Programmatic access to data and tools through the web using so-called web services has an important role to play in bioinformatics. In this article, we discuss the most popular approaches based on SOAP/WS-I and REST and describe our, a cross section of the community, experiences with providing and using web services in the context of biological sequence analysis. We briefly review main technological approaches as well as best practice hints that are useful for both users and developers. Finally, syntactic and semantic data integration issues with multiple web services are discussed.

Calling International Rescue: knowledge lost in literature and data landslide!

We live in interesting times. Portents of impending catastrophe pervade the literature, calling us to action in the face of unmanageable volumes of scientific data. But it isn't so much data generation per se, but the systematic burial of the knowledge embodied in those data that poses the problem: there is so much information available that we simply no longer know what we know, and finding what we want is hard - too hard. The knowledge we seek is often fragmentary and disconnected, spread thinly across thousands of databases and millions of articles in thousands of journals. The intellectual energy required to search this array of data-archives, and the time and money this wastes, has led several researchers to challenge the methods by which we traditionally commit newly acquired facts and knowledge to the scientific record. We present some of these initiatives here - a whirlwind tour of recent projects to transform scholarly publishing paradigms, culminating in Utopia and the Semantic Biochemical Journal experiment. With their promises to provide new ways of interacting with the literature, and new and more powerful tools to access and extract the knowledge sequestered within it, we ask what advances they make and what obstacles to progress still exist? We explore these questions, and, as you read on, we invite you to engage in an experiment with us, a real-time test of a new technology to rescue data from the dormant pages of published documents. We ask you, please, to read the instructions carefully. The time has come: you may turn over your papers...

An investigation into the effects of a virtual reality system on phantom limb pain: a pilot study.

BACKGROUND: There is no first-line treatment available for phantom limb pain (PLP). For some years, there has been interest in the use of mirrors and other techniques based on visual feedback. Unfortunately, up until now, all published studies have had methodological weaknesses with two recent systematic reviews concluding that therapies of this kind need more evidence to support their use. AIM: To evaluate the effects of a virtual reality (VR) activity on PLP. METHODS: This was a prospective pilot study of upper limb amputees using questionnaires to evaluate a VR system. Eleven participants were recruited, with nine completing all three sessions of VR. Participants undertook three sessions of VR, one a month for 3 months. Outcome measures were PLP pain intensity using an 11-point numerical rating scale (NRS), number of PLP episodes and duration of the PLP episodes. All participants were also asked for their judgement of change. Open-ended questions captured the qualitative experience of all aspects of the VR experience. RESULTS: The mean PLP pain score following three VR sessions reduced (6.11 v 3.56) but this was not a statistical difference (t = 2.1, df = 8, p = 0.07). No statistical difference was found for the number of PLP episodes (Pearson chi-square = 3.43, df = 2, p = 0.18) or the duration of each PLP episode (Pearson chi-square = 22.50, df = 16, p = 0.13). Three groups emerged: those whose pain reduced (the majority), those whose pain remained the same (small number) and one those whose pain increased slightly. DISCUSSION: There is insufficient evidence from these results to identify an effect of VR on PLP; however, this is a small group and qualitatively most were content with the treatment and wanted a longer trial.

Visualising biological data: a semantic approach to tool and database integration.

MOTIVATION: In the biological sciences, the need to analyse vast amounts of information has become commonplace. Such large-scale analyses often involve drawing together data from a variety of different databases, held remotely on the internet or locally on in-house servers. Supporting these tasks are ad hoc collections of data-manipulation tools, scripting languages and visualisation software, which are often combined in arcane ways to create cumbersome systems that have been customized for a particular purpose, and are consequently not readily adaptable to other uses. For many day-to-day bioinformatics tasks, the sizes of current databases, and the scale of the analyses necessary, now demand increasing levels of automation; nevertheless, the unique experience and intuition of human researchers is still required to interpret the end results in any meaningful biological way. Putting humans in the loop requires tools to support real-time interaction with these vast and complex data-sets. Numerous tools do exist for this purpose, but many do not have optimal interfaces, most are effectively isolated from other tools and databases owing to incompatible data formats, and many have limited real-time performance when applied to realistically large data-sets: much of the user's cognitive capacity is therefore focused on controlling the software and manipulating esoteric file formats rather than on performing the research. METHODS: To confront these issues, harnessing expertise in human-computer interaction (HCI), high-performance rendering and distributed systems, and guided by bioinformaticians and end-user biologists, we are building reusable software components that, together, create a toolkit that is both architecturally sound from a computing point of view, and addresses both user and developer requirements. Key to the system's usability is its direct exploitation of semantics, which, crucially, gives individual components knowledge of their own functionality and allows them to interoperate seamlessly, removing many of the existing barriers and bottlenecks from standard bioinformatics tasks. RESULTS: The toolkit, named Utopia, is freely available from http://utopia.cs.man.ac.uk/.

Defrosting the digital library: bibliographic tools for the next generation web.

Many scientists now manage the bulk of their bibliographic information electronically, thereby organizing their publications and citation material from digital libraries. However, a library has been described as "thought in cold storage," and unfortunately many digital libraries can be cold, impersonal, isolated, and inaccessible places. In this Review, we discuss the current chilly state of digital libraries for the computational biologist, including PubMed, IEEE Xplore, the ACM digital library, ISI Web of Knowledge, Scopus, Citeseer, arXiv, DBLP, and Google Scholar. We illustrate the current process of using these libraries with a typical workflow, and highlight problems with managing data and metadata using URIs. We then examine a range of new applications such as Zotero, Mendeley, Mekentosj Papers, MyNCBI, CiteULike, Connotea, and HubMed that exploit the Web to make these digital libraries more personal, sociable, integrated, and accessible places. We conclude with how these applications may begin to help achieve a digital defrost, and discuss some of the issues that will help or hinder this in terms of making libraries on the Web warmer places in the future, becoming resources that are considerably more useful to both humans and machines.

A network architecture supporting consistent rich behavior in collaborative interactive applications.

Network architectures for collaborative virtual reality have traditionally been dominated by client-server and peer-to-peer approaches, with peer-to-peer strategies typically being favored where minimizing latency is a priority, and client-server where consistency is key. With increasingly sophisticated behavior models and the demand for better support for haptics, we argue that neither approach provides sufficient support for these scenarios and, thus, a hybrid architecture is required. We discuss the relative performance of different distribution strategies in the face of real network conditions and illustrate the problems they face. Finally, we present an architecture that successfully meets many of these challenges and demonstrate its use in a distributed virtual prototyping application which supports simultaneous collaboration for assembly, maintenance, and training applications utilizing haptics.

Anatomy of BioJS, an open source community for the life sciences.

BioJS is an open source software project that develops visualization tools for different types of biological data. Here we report on the factors that influenced the growth of the BioJS user and developer community, and outline our strategy for building on this growth. The lessons we have learned on BioJS may also be relevant to other open source software projects.

Transfer of route learning from virtual to real environments.

The authors investigated the extent to which route learning in a virtual environment (VE) transfers to the real world. In Experiment 1, active VE exploration, on its own or with a map, produced better transfer of training than either no VE training at all or passive VE training; however, transfer was achieved after shorter training times with the map. Experiment 2 demonstrated that VE + map training was not superior to training with a map alone, and Experiment 3 demonstrated that the poorer performances observed after passive VE training were not simply due to a lack of attention but to the lack of active navigational decisions. The authors concluded that the present VE technology does not provide better route learning than studying a map.

Scientific competency questions as the basis for semantically enriched open pharmacological space development.

Molecular information systems play an important part in modern data-driven drug discovery. They do not only support decision making but also enable new discoveries via association and inference. In this review, we outline the scientific requirements identified by the Innovative Medicines Initiative (IMI) Open PHACTS consortium for the design of an open pharmacological space (OPS) information system. The focus of this work is the integration of compound-target-pathway-disease/phenotype data for public and industrial drug discovery research. Typical scientific competency questions provided by the consortium members will be analyzed based on the underlying data concepts and associations needed to answer the questions. Publicly available data sources used to target these questions as well as the need for and potential of semantic web-based technology will be presented.

Low-complexity regions within protein sequences have position-dependent roles.

BACKGROUND: Regions of protein sequences with biased amino acid composition (so-called Low-Complexity Regions (LCRs)) are abundant in the protein universe. A number of studies have revealed that i) these regions show significant divergence across protein families; ii) the genetic mechanisms from which they arise lends them remarkable degrees of compositional plasticity. They have therefore proved difficult to compare using conventional sequence analysis techniques, and functions remain to be elucidated for most of them. Here we undertake a systematic investigation of LCRs in order to explore their possible functional significance, placed in the particular context of Protein-Protein Interaction (PPI) networks and Gene Ontology (GO)-term analysis. RESULTS: In keeping with previous results, we found that LCR-containing proteins tend to have more binding partners across different PPI networks than proteins that have no LCRs. More specifically, our study suggests i) that LCRs are preferentially positioned towards the protein sequence extremities and, in contrast with centrally-located LCRs, such terminal LCRs show a correlation between their lengths and degrees of connectivity, and ii) that centrally-located LCRs are enriched with transcription-related GO terms, while terminal LCRs are enriched with translation and stress response-related terms. CONCLUSIONS: Our results suggest not only that LCRs may be involved in flexible binding associated with specific functions, but also that their positions within a sequence may be important in determining both their binding properties and their biological roles.

Performance of a skilled motor task in virtual and real environments.

Three experiments compared the performances of adult participants (three groups of 10) on a perceptuo-motor task in both real world (RW) and virtual environments (VEs). The task involved passing a hoop over a bent wire course, and three versions of the task were used: a 3-D wire course with no background, a flattened version of the 3-D course (2(1/2)-D course) with no background, and the 2(1/2)-D course with added background to provide spatial context. In all three experiments the participants had to prevent the hoop from touching the wire as they moved it. In the first experiment, the VE condition produced about 18 times more errors than the RW task. The VE 2(1/2)-D task was found to be as difficult as the 3-D, and the 2(1/2)-D with the added background produced more errors than the other two experiments. Taken together, the experiments demonstrate the difficulty of performing fine motor tasks in VEs, a phenomenon that has not been given due attention in many previous studies of motor control in VEs.