FAIR-compliant clinical, radiomics and DICOM metadata of RIDER, interobserver, Lung1 and head-Neck1 TCIA collections

Purpose: One of the most frequently cited radiomics investigations showed that features automatically extracted from routine clinical images could be used in prognostic modeling. These images have been made publicly accessible via The Cancer Imaging Archive (TCIA). There have been numerous requests for additional explanatory metadata on the following datasets — RIDER, Interobserver, Lung1, and Head–Neck1. To support repeatability, reproducibility, generalizability, and transparency in radiomics research, we publish the subjects’ clinical data, extracted radiomics features, and digital imaging and communications in medicine (DICOM) headers of these four datasets with descriptive metadata, in order to be more compliant with findable, accessible, interoperable, and reusable (FAIR) data management principles. Acquisition and validation methods: Overall survival time intervals were updated using a national citizens registry after internal ethics board approval. Spatial offsets of the primary gross tumor volume (GTV) regions of interest (ROIs) associated with the Lung1 CT series were improved on the TCIA. GTV radiomics features were extracted using the open-source Ontology-Guided Radiomics Analysis Workflow (O-RAW). We reshaped the output of O-RAW to map features and extraction settings to the latest version of Radiomics Ontology, so as to be consistent with the Image Biomarker Standardization Initiative (IBSI). Digital imaging and communications in medicine metadata was extracted using a research version of Semantic DICOM (SOHARD, GmbH, Fuerth; Germany). Subjects’ clinical data were described with metadata using the Radiation Oncology Ontology. All of the above were published in Resource Descriptor Format (RDF), that is, triples. Example SPARQL queries are shared with the reader to use on the online triples archive, which are intended to illustrate how to exploit this data submission. Data format: The accumulated RDF data are publicly accessible through a SPARQL endpoint where the triples are archived. The endpoint is remotely queried through a graph database web application at http://sparql.cancerdata.org. SPARQL queries are intrinsically federated, such that we can efficiently cross-reference clinical, DICOM, and radiomics data within a single query, while being agnostic to the original data format and coding system. The feder

Quantitative imaging in radiation oncology

Artificially intelligent eyes, built on machine and deep learning technologies, can empower our capability of analysing patients’ images. By revealing information invisible at our eyes, we can build decision aids that help our clinicians to provide more effective treatment, while reducing side effects. The power of these decision aids is to be based on patient tumour biologically unique properties, referred to as biomarkers. To fully translate this technology into the clinic we need to overcome barriers related to the reliability of image-derived biomarkers, trustiness in AI algorithms and privacy-related issues that hamper the validation of the biomarkers. This thesis developed methodologies to solve the presented issues, defining a road map for the responsible usage of quantitative imaging into the clinic as decision support system for better patient care

Report on shape analysis and matching and on semantic matching

In GRAVITATE, two disparate specialities will come together in one working platform for the archaeologist: the fields of shape analysis, and of metadata search. These fields are relatively disjoint at the moment, and the research and development challenge of GRAVITATE is precisely to merge them for our chosen tasks. As shown in chapter 7 the small amount of literature that already attempts join 3D geometry and semantics is not related to the cultural heritage domain. Therefore, after the project is done, there should be a clear ‘before-GRAVITATE’ and ‘after-GRAVITATE’ split in how these two aspects of a cultural heritage artefact are treated.This state of the art report (SOTA) is ‘before-GRAVITATE’. Shape analysis and metadata description are described separately, as currently in the literature and we end the report with common recommendations in chapter 8 on possible or plausible cross-connections that suggest themselves. These considerations will be refined for the Roadmap for Research deliverable.Within the project, a jargon is developing in which ‘geometry’ stands for the physical properties of an artefact (not only its shape, but also its colour and material) and ‘metadata’ is used as a general shorthand for the semantic description of the provenance, location, ownership, classification, use etc. of the artefact. As we proceed in the project, we will find a need to refine those broad divisions, and find intermediate classes (such as a semantic description of certain colour patterns), but for now the terminology is convenient – not least because it highlights the interesting area where both aspects meet.On the ‘geometry’ side, the GRAVITATE partners are UVA, Technion, CNR/IMATI; on the metadata side, IT Innovation, British Museum and Cyprus Institute; the latter two of course also playing the role of internal users, and representatives of the Cultural Heritage (CH) data and target user’s group. CNR/IMATI’s experience in shape analysis and similarity will be an important bridge between the two worlds for geometry and metadata. The authorship and styles of this SOTA reflect these specialisms: the first part (chapters 3 and 4) purely by the geometry partners (mostly IMATI and UVA), the second part (chapters 5 and 6) by the metadata partners, especially IT Innovation while the joint overview on 3D geometry and semantics is mainly by IT Innovation and IMATI. The common section on Perspectives was written with the contribution of all

The Palgrave Handbook of Digital Russia Studies

This open access handbook presents a multidisciplinary and multifaceted perspective on how the ‘digital’ is simultaneously changing Russia and the research methods scholars use to study Russia. It provides a critical update on how Russian society, politics, economy, and culture are reconfigured in the context of ubiquitous connectivity and accounts for the political and societal responses to digitalization. In addition, it answers practical and methodological questions in handling Russian data and a wide array of digital methods. The volume makes a timely intervention in our understanding of the changing field of Russian Studies and is an essential guide for scholars, advanced undergraduate and graduate students studying Russia today

The Palgrave Handbook of Digital Russia Studies

This open access handbook presents a multidisciplinary and multifaceted perspective on how the ‘digital’ is simultaneously changing Russia and the research methods scholars use to study Russia. It provides a critical update on how Russian society, politics, economy, and culture are reconfigured in the context of ubiquitous connectivity and accounts for the political and societal responses to digitalization. In addition, it answers practical and methodological questions in handling Russian data and a wide array of digital methods. The volume makes a timely intervention in our understanding of the changing field of Russian Studies and is an essential guide for scholars, advanced undergraduate and graduate students studying Russia today

Usage-driven Maintenance of Knowledge Organization Systems

Knowledge Organization Systems (KOS) are typically used as background knowledge for document indexing in information retrieval. They have to be maintained and adapted constantly to reflect changes in the domain and the terminology. In this thesis, approaches are provided that support the maintenance of hierarchical knowledge organization systems, like thesauri, classifications, or taxonomies, by making information about the usage of KOS concepts available to the maintainer. The central contribution is the ICE-Map Visualization, a treemap-based visualization on top of a generalized statistical framework that is able to visualize almost arbitrary usage information. The proper selection of an existing KOS for available documents and the evaluation of a KOS for different indexing techniques by means of the ICE-Map Visualization is demonstrated. For the creation of a new KOS, an approach based on crowdsourcing is presented that uses feedback from Amazon Mechanical Turk to relate terms hierarchically. The extension of an existing KOS with new terms derived from the documents to be indexed is performed with a machine-learning approach that relates the terms to existing concepts in the hierarchy. The features are derived from text snippets in the result list of a web search engine. For the splitting of overpopulated concepts into new subconcepts, an interactive clustering approach is presented that is able to propose names for the new subconcepts. The implementation of a framework is described that integrates all approaches of this thesis and contains the reference implementation of the ICE-Map Visualization. It is extendable and supports the implementation of evaluation methods that build on other evaluations. Additionally, it supports the visualization of the results and the implementation of new visualizations. An important building block for practical applications is the simple linguistic indexer that is presented as minor contribution. It is knowledge-poor and works without any training. This thesis applies computer science approaches in the domain of information science. The introduction describes the foundations in information science; in the conclusion, the focus is set on the relevance for practical applications, especially regarding the handling of different qualities of KOSs due to automatic and semiautomatic maintenance

ECLAP 2012 Conference on Information Technologies for Performing Arts, Media Access and Entertainment

It has been a long history of Information Technology innovations within the Cultural Heritage areas. The Performing arts has also been enforced with a number of new innovations which unveil a range of synergies and possibilities. Most of the technologies and innovations produced for digital libraries, media entertainment and education can be exploited in the field of performing arts, with adaptation and repurposing. Performing arts offer many interesting challenges and opportunities for research and innovations and exploitation of cutting edge research results from interdisciplinary areas. For these reasons, the ECLAP 2012 can be regarded as a continuation of past conferences such as AXMEDIS and WEDELMUSIC (both pressed by IEEE and FUP). ECLAP is an European Commission project to create a social network and media access service for performing arts institutions in Europe, to create the e-library of performing arts, exploiting innovative solutions coming from the ICT