Alexander Garcia

BioJS: an open source JavaScript framework for biological data visualization.

SUMMARY BioJS is an open-source project whose main objective is the visualization of biological data in JavaScript. BioJS provides an easy-to-use consistent framework for bioinformatics application programmers. It follows a community-driven standard specification that includes a collection of components purposely designed to require a very simple configuration and installation. In addition to the programming framework, BioJS provides a centralized repository of components available for reutilization by the bioinformatics community. AVAILABILITY AND IMPLEMENTATION http://code.google.com/p/biojs/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

Dasty2, an Ajax protein DAS client

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/.

BioJS: an open source standard for biological visualisation - its status in 2014.

BioJS is a community-based standard and repository of functional components to represent biological information on the web. The development of BioJS has been prompted by the growing need for bioinformatics visualisation tools to be easily shared, reused and discovered. Its modular architecture makes it easy for users to find a specific functionality without needing to know how it has been built, while components can be extended or created for implementing new functionality. The BioJS community of developers currently provides a range of functionality that is open access and freely available. A registry has been set up that categorises and provides installation instructions and testing facilities at http://www.ebi.ac.uk/tools/biojs/. The source code for all components is available for ready use at https://github.com/biojs/biojs.

Biotea: RDFizing PubMed Central in Support for the Paper as an Interface to the Web of Data

BackgroundThe World Wide Web has become a dissemination platform for scientific and non-scientific publications. However, most of the information remains locked up in discrete documents that are not always interconnected or machine-readable. The connectivity tissue provided by RDF technology has not yet been widely used to support the generation of self-describing, machine-readable documents.ResultsIn this paper, we present our approach to the generation of self-describing machine-readable scholarly documents. We understand the scientific document as an entry point and interface to the Web of Data. We have semantically processed the full-text, open-access subset of PubMed Central. Our RDF model and resulting dataset make extensive use of existing ontologies and semantic enrichment services. We expose our model, services, prototype, and datasets at http://biotea.idiginfo.org/ConclusionsThe semantic processing of biomedical literature presented in this paper embeds documents within the Web of Data and facilitates the execution of concept-based queries against the entire digital library. Our approach delivers a flexible and adaptable set of tools for metadata enrichment and semantic processing of biomedical documents. Our model delivers a semantically rich and highly interconnected dataset with self-describing content so that software can make effective use of it.

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. DOI: http://dx.doi.org/10.7554/eLife.07009.001

Dasty3, a WEB framework for DAS

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

Developing Ontologies within Decentralised Settings

This chapter addresses two research questions: “How should a well-engineered methodology facilitate the development of ontologies within communities of practice?” and “What methodology should be used?” If ontologies are to be developed by communities then the ontology development life cycle should be better understood within this context. This chapter presents the Melting Point (MP), a proposed new methodology for developing ontologies within decentralised settings. It describes how MP was developed by taking best practices from other methodologies, provides details on recommended steps and recommended processes, and compares MP with alternatives. The methodology presented here is the product of direct first-hand experience and observation of biological communities of practice in which some of the authors have been involved. The Melting Point is a methodology engineered for decentralised communities of practice for which the designers of technology and the users may be the same group. As such, MP provides a potential foundation for the establishment of standard practices for ontology engineering.

Social Tags and Linked Data for Ontology Development: A Case Study in the Financial Domain

We describe a domain ontology development approach that extracts domain terms from folksonomies and enrich them with data and vocabularies from the Linked Open Data cloud. As a result, we obtain lightweight domain ontologies that combine the emergent knowledge of social tagging systems with formal knowledge from Ontologies. In order to illustrate the feasibility of our approach, we have produced an ontology in the financial domain from tags available in Delicious, using DBpedia, OpenCyc and UMBEL as additional knowledge sources.

Tags4Tags: Using Tagging to Consolidate Tags

Tagging has become increasingly popular and useful across various social networks and applications. It allows users to classify and organize resources for improving the retrieval performance over those tagged resources. Within social networks, tags can also facilitate the interaction between members of the community, e.g. because similar tags may represent similar interests. Although obviously useful for straightforward retrieval tasks, the current meta-data model underlying typical tagging systems does not fully exploit the potential of the social process of finding, establishing, challenging, and promoting symbols, i.e. tags. For instance, the social process is not used for establishing an explicit hierarchy of tags or for the collective detection of equivalencies, synonyms, morphological variants, and other useful relationships across tags. This limitation is due to the constraints of the typical meta-model of tagging, in which the subject must be a Web resource, the relationship type is always hasTag, and the object must be a tag as a literal. In this paper, we propose a simple yet effective extension for the current meta-model of tagging systems in order to exploit the potential of collective tagging for the emergence of richer semantic structures, in particular for capturing semantic relationships between tags. Our approach expands the range of the object of tagging from Web resources only to the union of (1) Web resources and (2) pairs of tags, i.e., users can now use arbitrary tags for expressing typed relationships between a pair of tags. This allows the user community to establish similarity relations and other types of relationships between tags. We present a first prototype and the results from an evaluation in a small controlled setting.

OntoDas – a tool for facilitating the construction of complex queries to the Gene Ontology

BackgroundOntologies 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.ResultsOntoDas 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.ConclusionOntoDas 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