Browsing by Author "Salazar, Gustavo A"

Now showing 1 - 5 of 5
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    Open Access
    DAS Writeback: A collaborative annotation system for proteins
    (2010) Salazar, Gustavo A; Blake, Edwin H
    We designed and developed a Collaborative Annotation System for Proteins called DAS Writeback, which extends the Distributed Annotation System (DAS) to provide the functionalities of adding, editing and deleting annotations. A great deal of e ort has gone into gathering information about proteins over the last few years. By June 2009, UniProtKB/Swiss-Prot, a curated database, contained over four hundred thousand sequence entries and UniProtKB/TrEMBL, a database with automated annotation, contained over eight million sequence entries. Every protein is annotated with relevant information, which needs to be e ciently captured and made available to other research groups. These include annotations about the structure, the function or the biochemical residues. Several research groups have taken on the task of making this information accessible to the community, however, information ow in the opposite direction has not been extensively explored. Users are currently passive actors that behave as consumers of one or several sources of protein annotations and they have no immediate way to provide feedback to the source if, for example, a mistake is detected or they want to add information. Any change has to be done by the owner of the database. The current lack of being able to feed information back to a database is tackled in this project. The solution consists of an extension of the DAS protocol that de nes the communication rules between the client and the writeback server following the Uniform Interface of the RESTful architecture. A protocol extension was proposed to the DAS community and implementations of both server and client were created in order to have a fully functional system. For the development of the server, writing functionalities were added to MyDAS, which is a widely used DAS server. The writeback client is an extended version of the web-based protein client Dasty2. The involvement of the DAS community and other potential users was a fundamental component of this project. The architecture was designed with the insight of the DAS specialized forum, a prototype was then created and subsequently presented in the DAS workshop 2009. The feedback from the forum and workshop was used to rede ne the architecture and implement the system. A usability experiment was performed using potential users of the system emulating a real annotation task. It demonstrated that DAS writeback is e ective, usable and will provide the appropriate environment for the creation and evolution of a protein annotation community. Although the scope of this research is limited to protein annotations, the speci cation was de ned in a general way. It can, therefore, be used for other types of information supported by DAS, implying that the server is versatile enough to be used in other scenarios without major modi cations.
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    Integration and visualisation of data in bioinformatics
    (2015) Salazar, Gustavo A; Mulder Nicola
    The most recent advances in laboratory techniques aimed at observing and measuring biological processes are characterised by their ability to generate large amounts of data. The more data we gather, the greater the chance of finding clues to understand the systems of life. This, however, is only true if the methods that analyse the generated data are efficient, effective, and robust enough to overcome the challenges intrinsic to the management of big data. The computational tools designed to overcome these challenges should also take into account the requirements of current research. Science demands specialised knowledge for understanding the particularities of each study; in addition, it is seldom possible to describe a single observation without considering its relationship with other processes, entities or systems. This thesis explores two closely related fields: the integration and visualisation of biological data. We believe that these two branches of study are fundamental in the creation of scientific software tools that respond to the ever increasing needs of researchers. The distributed annotation system (DAS) is a community project that supports the integration of data from federated sources and its visualisation on web and stand-alone clients. We have extended the DAS protocol to improve its search capabilities and also to support feature annotation by the community. We have also collaborated on the implementation of MyDAS, a server to facilitate the publication of biological data following the DAS protocol, and contributed in the design of the protein DAS client called DASty. Furthermore, we have developed a tool called probeSearcher, which uses the DAS technology to facilitate the identification of microarray chips that include probes for regions on proteins of interest. Another community project in which we participated is BioJS, an open source library of visualisation components for biological data. This thesis includes a description of the project, our contributions to it and some developed components that are part of it. Finally, and most importantly, we combined several BioJS components over a modular architecture to create PINV, a web based visualiser of protein-protein interaction (PPI) networks, that takes advantage of the features of modern web technologies in order to explore PPI datasets on an almost ubiquitous platform (the web) and facilitates collaboration between scientific peers. This thesis includes a description of the design and development processes of PINV, as well as current use cases that have benefited from the tool and whose feedback has been the source of several improvements to PINV. Collectively, this thesis describes novel software tools that, by using modern web technologies, facilitates the integration, exploration and visualisation of biological data, which has the potential to contribute to our understanding of the systems of life.
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    MyDas, an extensible Java DAS server
    (Public Library of Science, 2012) Salazar, Gustavo A; García, Leyla J; Jones, Philip; Jimenez, Rafael C; Quinn, Antony F; Jenkinson, Andrew M; Mulder, Nicola; Martin, Maria; Hunter, Sarah; Hermjakob, Henning
    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.
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    myKaryoView: a light-weight client for visualization of genomic data
    (Public Library of Science, 2011) Jimenez, Rafael C; Salazar, Gustavo A; Gel, Bernat; Dopazo, Joaquin; Mulder, Nicola; Corpas, Manuel
    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 .
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    A web-based protein interaction network visualizer
    (BioMed Central, 2014-05-06) Salazar, Gustavo A; Meintjes, Ayton; Mazandu, Gaston K; Rapanoël, Holifidy A; Akinola, Richard O; Mulder, Nicola J
    Abstract Background Interaction between proteins is one of the most important mechanisms in the execution of cellular functions. The study of these interactions has provided insight into the functioning of an organism’s processes. As of October 2013, Homo sapiens had over 170000 Protein-Protein interactions (PPI) registered in the Interologous Interaction Database, which is only one of the many public resources where protein interactions can be accessed. These numbers exemplify the volume of data that research on the topic has generated. Visualization of large data sets is a well known strategy to make sense of information, and protein interaction data is no exception. There are several tools that allow the exploration of this data, providing different methods to visualize protein network interactions. However, there is still no native web tool that allows this data to be explored interactively online. Results Given the advances that web technologies have made recently it is time to bring these interactive views to the web to provide an easily accessible forum to visualize PPI. We have created a Web-based Protein Interaction Network Visualizer: PINV, an open source, native web application that facilitates the visualization of protein interactions ( http://biosual.cbio.uct.ac.za/pinv.html ). We developed PINV as a set of components that follow the protocol defined in BioJS and use the D3 library to create the graphic layouts. We demonstrate the use of PINV with multi-organism interaction networks for a predicted target from Mycobacterium tuberculosis, its interacting partners and its orthologs. Conclusions The resultant tool provides an attractive view of complex, fully interactive networks with components that allow the querying, filtering and manipulation of the visible subset. Moreover, as a web resource, PINV simplifies sharing and publishing, activities which are vital in today’s research collaborative environments. The source code is freely available for download at https://github.com/4ndr01d3/biosual .