Browsing by Author "Jimenez, Rafael"

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    Open Access
    DAS Writeback: A Collaborative Annotation System
    (BioMed Central Ltd, 2011) Salazar, Gustavo; Jimenez, Rafael; Garcia, Alexander; Hermjakob, Henning; Mulder, Nicola; Blake, Edwin
    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.
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    Open Access
    OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology
    (BioMed Central Ltd, 2008) O'Neill, Kieran; Garcia, Alexander; Schwegmann, Anita; Jimenez, Rafael; Jacobson, Dan; Hermjakob, Henning
    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