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1.  EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats 
Bioinformatics  2013;29(10):1325-1332.
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
doi:10.1093/bioinformatics/btt113
PMCID: PMC3654706  PMID: 23479348
2.  NucleaRDB: information system for nuclear receptors 
Nucleic Acids Research  2011;40(Database issue):D377-D380.
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.
doi:10.1093/nar/gkr960
PMCID: PMC3245090  PMID: 22064856
3.  Integrating GPCR-specific information with full text articles 
BMC Bioinformatics  2011;12:362.
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.
doi:10.1186/1471-2105-12-362
PMCID: PMC3179973  PMID: 21910883
4.  BioXSD: the common data-exchange format for everyday bioinformatics web services 
Bioinformatics  2010;26(18):i540-i546.
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.
Contact: matus.kalas@bccs.uib.no; developers@bioxsd.org; support@bioxsd.org
doi:10.1093/bioinformatics/btq391
PMCID: PMC2935419  PMID: 20823319
5.  BioCatalogue: a universal catalogue of web services for the life sciences 
Nucleic Acids Research  2010;38(Web Server issue):W689-W694.
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.
doi:10.1093/nar/gkq394
PMCID: PMC2896129  PMID: 20484378
6.  The EMBRACE web service collection 
Nucleic Acids Research  2010;38(Web Server issue):W683-W688.
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.
doi:10.1093/nar/gkq297
PMCID: PMC2896104  PMID: 20462862
7.  Low-complexity regions within protein sequences have position-dependent roles 
BMC Systems Biology  2010;4:43.
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.
doi:10.1186/1752-0509-4-43
PMCID: PMC2873317  PMID: 20385029
8.  Calling International Rescue: knowledge lost in literature and data landslide! 
Biochemical Journal  2009;424(Pt 3):317-333.
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…
doi:10.1042/BJ20091474
PMCID: PMC2805925  PMID: 19929850
dynamic document content; interactive PDF; linking documents with research data; manuscript mark-up; mark-up standards; semantic publishing; BJ, Biochemical Journal; COHSE, Conceptual Open Hypermedia Services Environment; DOI, Digital Object Identifier; GO, Gene Ontology; GPCR, G protein-coupled receptor; HTML, HyperText Mark-up Language; IUPAC, International Union of Pure and Applied Chemistry; NTD, Neglected Tropical Diseases; OBO, Open Biomedical Ontologies; PDB, Protein Data Bank; PDF, Portable Document Format; PLoS, Public Library of Science; PMC, PubMed Central; PTM, post-translational modification; RSC, Royal Society of Chemistry; SDA, Structured Digital Abstract; STM, Scientific, Technical and Medical; UD, Utopia Documents; XML, eXtensible Mark-up Language; XMP, eXtensible Metadata Platform
9.  Experience using web services for biological sequence analysis 
Briefings in Bioinformatics  2008;9(6):493-505.
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.
doi:10.1093/bib/bbn029
PMCID: PMC2989672  PMID: 18621748
web services; SOAP; REST; internet technologies; sequence analysis
10.  Visualising biological data: a semantic approach to tool and database integration 
BMC Bioinformatics  2009;10(Suppl 6):S19.
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 customised 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 .
doi:10.1186/1471-2105-10-S6-S19
PMCID: PMC2697642  PMID: 19534744
11.  Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web 
PLoS Computational Biology  2008;4(10):e1000204.
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.
doi:10.1371/journal.pcbi.1000204
PMCID: PMC2568856  PMID: 18974831

Results 1-11 (11)