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Visual exploration of clustered data., Presentation Slides for Clusterix: https://www.slideshare.net/eamonnmag/clusterix-at-vds-2016

In this paper, we reflect on the use of visualization techniques for analyzing electronic health record data with privacy concerns. Privacy-preserving data visualization is a relatively new area of research compared to the more established research areas of privacy-preserving data publishing and data mining. We describe the opportunities and challenges for privacy-preserving visualization of electronic health record data by analyzing the different disclosure risk types, and vulnerabilities associated with commonly used visualization techniques.

The digitalisation of information now affects most fields of human activity. From the social sciences to biology to physics, the volume, velocity, and variety of data exhibit exponential growth trends. With such rates of expansion, efforts to understand and make sense of datasets of such scale, how- ever driven and directed, progress only at an incremental pace. The challenges are significant. For instance, the ability to display an ever growing amount of data is physically and naturally bound by the dimensions of the average sized display. A synergistic interplay between statistical analysis and visualisation approaches outlines a path for significant advances in the field of data exploration. We can turn to statistics to provide principled guidance for prioritisation of information to display. Using statistical results, and combining knowledge from the cognitive sciences, visual techniques can be used to highlight salient data attributes. The purpose of this thesis is to explore the link between computer science, statistics, visualization, and the cognitive sciences, to define and develop more systematic approaches towards the design of glyphs. Glyphs represent the variables of multivariate data records by mapping those variables to one or more visual channels (e.g., colour, shape, and texture). They offer a unique, compact solution to the presentation of a large amount of multivariate information. However, composing a meaningful, interpretable, and learnable glyph can pose a number of problems. The first of these problems exist in the subjectivity involved in the process of data to visual channel mapping, and in the organisation of those visual channels to form the overall glyph. Our first contribution outlines a computational technique to help systematise many of these otherwise subjective elements of the glyph design process. For visual information compression, common patterns (motifs) in time series or graph data for example, may be replaced with more compact, visual representations. Glyph-based techniques can provide such representations that can help users find common patterns more quickly, and at the same time, bring attention to anomalous areas of the data. However, replacing any data with a glyph is not going to make tasks such as visual search easier. A key problem is the selection of semantically meaningful motifs with the potential to compress large amounts of information. A second contribution of this thesis is a computational process for systematic design of such glyph libraries and their subsequent glyphs. A further problem in the glyph design process is in their evaluation. Evaluation is typically a time-consuming, highly subjective process. Moreover, domain experts are not always plentiful, therefore obtaining statistically significant evaluation results is often difficult. A final contribution of this work is to investigate if there are areas of evaluation that can be performed computationally.

A curated, searchable portal of inter-related data standards, databases, and policies in the life, environmental and biomedical sciences: https://biosharing.org

A curated, searchable portal of inter-related data standards, databases, and policies in the life, environmental and biomedical scienceshttps://biosharing.org

A curated, searchable portal of inter-related data standards, databases, and policies in the life, environmental and biomedical sciences: https://biosharing.org

Find me the data - Discover and explore Springer Nature’s Scientific Data datasets with the ISA-explorer toolScientific Data is a Springer Nature journal focused on data publication. The main article type is a Data Descriptor, which depicts rigorously described, reusable datasets. Each Data Descriptor is accompanied by metadata represented in the ISA-Tab format, which is a tabular format following the Investigation/Study/Assay model. The ISA-explorer tool [1] uses the information in the Scientific Data ISA-Tab metadata files to facilitate dataset discovery. The tool allows users to filter datasets by different criteria: for example, a specific design type or data stored at a particular repository.. The filters can be combined in a boolean search allowing users to easily and quickly discover specific types of data. The ISA-explorer also offers a generic search box, allowing for keyword-based searches of the ISA-Tab metadata files. Additionally, the tool allows browsing of dataset specific information such as related publications and a visualisation of the distribution of the characteristics of the samples involved in the study generating the data. We have some improvements already planned; for example, showing overall statistics, supporting richer query searches considering the semantics of the data (e.g. query expansion based on synonyms) and relying on richer knowledge representations (such as linkedISA [2]). [1] http://blogs.nature.com/scientificdata/2015/12/17/isa-explorer/ [2] Alejandra González-Beltrán, Eamonn Maguire, Susanna-Assunta Sansone and Philippe Rocca-Serra. linkedISA: semantic representation of ISA-Tab experimental metadata. BMC Bioinformatics 2014, 15(Suppl 14):S4. http://dx.doi.org/10.1186/1471-2105-15-S14-S4URL to Project: http://scientificdata.isa-explorer.org/

Background As the size and complexity of scientific datasets and the corresponding information stores grow, standards for collecting, describing, formatting, submitting and exchanging information are playing an increasingly active role. Several initiatives occupy strategic positions in the international scenario, both within and across domains. However, the job of harmonising reporting standards is still very much a work in progress; both software interoperability and the data integration remain challenging as things stand. Results The status quo with respect to standardization initiatives is summarized here, with particular emphasis on the motivation for, and the challenges of, ongoing synergistic activities amongst the academic community focused on the creation of truly interoperable standards. Conclusions Groups generating standards should engage with ongoing cross-domain activities to simplify the integration of heterogeneous data sets to the greatest possible extent.

BioSharing poster - January 2015

BioSharing (http://www.biosharing.org) is a curated, web-based, searchable portal of three linked registries of content standards, databases and data policies in the life sciences, broadly encompassing the biological, natural and biomedical sciences. Our records are informative and discoverable, maximizing standards adoption and (re)use (e.g. in data policies), and allowing the monitoring of their maturity and evolution (Tenenbaum, Sansone, Haendel; Am Med Inform Assoc, 2014). With over 1,300 records, BioSharing content can be searched using simple or advanced searches, filtered via a filtering matrix, or grouped via the ‘Collection’ feature, according to field of interest or focus. Examples are the NPG Scientific Data and BioMedCentral Collections, collating and linking the recommended standards and repositories from their Data Policy for author. Similarly other publishers, projects and organizations are creating Collections by selecting and filtering standards and databases relevant to their work, such as the BD2K bioCADDIE project. As a community effort, BioSharing offers users the ability to ‘claim’ records, allowing their update. Each claimant also has a user profile that can be linked to their resources, publications and ORCID ID, thus providing visibility for them as an individual.Launched in 2011 as an extension and evolution of the MIBBI portal (founded by the same Operational Team, led by Sansone), BioSharing is working with a growing number of journals and other registries; it is also part of ELIXIR-UK Node and contributing to the NIH BD2K CEDAR. Driven by an international Advisory Board (co-chaired by Tenenbaum, Haendel) the BioSharing userbase has grown by 40% over the last year, thanks to successful engagement with researchers, publishers, librarians, developers and other stakeholders via several routes, including a joint RDA/Force11 working group (co-chaired by Lawrence and Hodson) and a collaboration with the International Biocuration Society.

ISA-tools poster - January 2015

BioSharing works to register well-constituted efforts developing biosciences standards and collaborate with other groups, portals and resources to progressively monitoring their: development, evolution and integration; implementation and use in databases; and adoption by data policies by funders and journals. Ultimately, by delivering an informative and discoverable resource, BioSharing is set to serve those seeking information on the existing standards for adoption, development and training purposes; but also to identify areas where duplications or gaps in coverage exist and promote harmonization to stop wasteful reinvention, where possible.

Curate, store, analyse, share and publish your bioscience experiment The open source ISA tools and its international community of users and collaborators

My sequence logo redesign for Biovis 2013. See link below for original sequence logo design and the spec for the competition. In this work, we investigate how the sequence logo could be improved from both the perspective of a bioinformatician and computer scientist and a biologist. We identify the major changes invoked alongside the effect we wished to invoke. In this design, we mixed a combination of the existing representation to decrease the time to learn and new glyph-based techniques to add additional information. We have kept colors in place as a mechanism of identifying the classes of amino acids (aliphatic, hydroxyl/sulphur containing, cyclic, aromatic, basic and acidic), where for example, blue corresponds to the basic group. The consistency between the old and new figure in using the same colours is seen as a way of reducing the time to learn this new technique. Letters are kept in the encoding since they are well known by the biologists, however we remove those letters that would be too small to show to reduce visual clutter. Rectangles are used to fill space relative to the presence of an amino acid instead of the stacked letter approach used in the origin figure. We believe that this removes problems with the original representation where more dense letters, e.g H or A would look bigger compared to an I even though the actual size was the same. Glyph visualisation techniques can be used to depict hydrophobicity of a region and general side-chain charge of the amino acids in the group. In our design we show these changes when there is a change between groups, see positions 4, 7 and 24, 27 in the figure showing changes in the liking of water. There are also some examples in changes in dominance of side-chain electrical charge at positions 24 and 29. We employ a technique published by Brandes et al. in 2013 termed GestaltLines (DOI 10.1111/cgf.12104) to give a simplified indication of region conservation. Through this technique, it is simple to see conserved regions without the need to parse any additional information in the image. The salient information, which in this case is conservation in regions of the protein are instantly accessible. We also use opacity to fade out highly unconserved regions to ease visual search. Moreover, each region is better separated visually for comparison purposes through the use of a light-grey background alternating with white.

In this paper, we present a user-centered design study on poetry visualization. We develop a rule-based solution to address the conflicting needs for maintaining the flexibility of visualizing a large set of poetic variables and for reducing the tedium and cognitive load in interacting with the visual mapping control panel. We adopt Munzner’s nested design model to maintain high-level interactions with the end users in a closed loop. In addition, we examine three design options for alleviating the difficulty in visualizing poems latitudinally. We present severalexample uses of poetry visualization in scholarly research on poetry. Presented at EuroVis 2013 in Leipzig, Germany.

BioSharing works to register well-constituted efforts developing biosciences standards and collaborate with other groups, portals and resources to progressively monitoring their: development, evolution and integration; implementation and use in databases; and adoption by data policies by funders and journals. Ultimately, by delivering an informative and discoverable resource, BioSharing is set to serve those seeking information on the existing standards for adoption, development and training purposes; but also to identify areas where duplications or gaps in coverage exist and promote harmonization to stop wasteful reinvention, where possible.

The abstract for our talk that will be presented at Digital Research 2013 - http://digital-research.oerc.ox.ac.uk/

Poster presented at BioVis 2011 on "Visualization of experimental design and workflows in biological experiments".

Taxonomies are core to our everyday working. We constantly categorize entities to aid our understanding and navigation of the world around us. In the most basic of cases, we may categorize animals into dangerous or non-dangerous, pets or pests and people into friends and strangers. Since time began, our ancestors have used taxonomy to stay away from things carrying the potential to cause harm, and it is shown that we have the ability to classify complex entities even as children through evolved parts of the human brain. This paper explores the origin of taxonomy and how it carries immense importance in our world, its importance in biology and how it is used in visualization also. This is a short paper reviewing taxonomy in biology and visualization. It is not perfect, but it is a comprehensive review.

The open source ISA software suite and its international community.