Semantic Metadata Annotation Services in the Biomedical Domain—A Literature Review

For all research data collected, data descriptions and information about the corresponding variables are essential for data analysis and reuse. To enable cross-study comparisons and analyses, semantic interoperability of metadata is one of the most important requirements. In the area of clinical and epidemiological studies, data collection instruments such as case report forms (CRFs), data dictionaries and questionnaires are critical for metadata collection. Even though data collection instruments are often created in a digital form, they are mostly not machine readable; i.e., they are not semantically coded. As a result, the comparison between data collection instruments is complex. The German project NFDI4Health is dedicated to the development of national research data infrastructure for personal health data, and as such searches for ways to enhance semantic interoperability. Retrospective integration of semantic codes into study metadata is important, as ongoing or completed studies contain valuable information. However, this is labor intensive and should be eased by software. To understand the market and find out what techniques and technologies support retrospective semantic annotation/enrichment of metadata, we conducted a literature review. In NFDI4Health, we identified basic requirements for semantic metadata annotation software in the biomedical field and in the context of the FAIR principles. Ten relevant software systems were summarized and aligned with those requirements. We concluded that despite active research on semantic annotation systems, no system meets all requirements. Consequently, further research and software development in this area is needed, as interoperability of data dictionaries, questionnaires and data collection tools is key to reusing and combining results from independent research studies.

Saudi women driving: images, stereotyping and digital media

This article examines the representations of Saudi women driving that circulated shortly after the lifting of the ban and considers the social, commercial and technological forces that helped to shape those representations . A corpus of images was collected from two international image banks – Getty and Shutterstock – as well as from a Google Image search. The images use Van Leeuwen’s (2008) visual representation framework in Discourse and Practice: New Tools for Critical Analysis, paying particular attention to the similarities and differences between the images available in the image banks and those that were made prominent in the Google search. In addition, semantic metadata accompanying these images were also analysed in order to understand the linguistic constraints that had been put on searches for these images and the ontologies of the issue that they promoted. Finally, a more detailed analysis was performed on images that had been appropriated into different contexts such as news stories and advertisements to investigate how these images were adapted to support different political, cultural and commercial agendas. Findings suggest that images of Saudi women that circulated online internationally shortly after the lifting of the ban were mostly generic and decontextualized, creating simplified and trivialized depictions of gender relations and social change in the Kingdom. The analysis shows how commercial concerns which influence both the creation of stock images and the way they are taken up by news organizations and advertisers can sometimes have the effect of erasing the complexity of political events and reinforcing the very stereotypes they seem to be challenging.

FOLKSONOMIA EM REPOSITÓRIOS DIGITAIS: análise da produção científica nacional e internacional = FOLKSONOMY IN DIGITAL REPOSITORIES: analysis of national and international scientific production

Estuda aspectos concernentes à Folksonomia e à representação colaborativa da informação em sistemas como os Repositórios Digitais. Tem como objetivo analisar a produção científica nacional e internacional sobre Folksonomia em Repositórios Digitais. Objetiva especificamente: demonstrar o status das produções científicas sobre essa temática; categorizar os enfoques de estudos acerca da temática e apresentar as tendências e perspectivas de estudos sobre o tema. Tem como metodologia as pesquisas bibliográfica, exploratória e descritiva com abordagem quantitativa e qualitativa para fins de recuperação, análise e mapeamento da produção científica nacional e internacional sobre a temática no Portal de Periódicos CAPES. Constata que 53% das produções científicas recuperadas foram publicadas no período de 2010 a 2015 e 47% dos trabalhos estão distribuídos no intervalo de tempo entre 2016 a 2020. Evidencia que, dentre os artigos recuperados, 17% são pesquisas publicadas em periódicos brasileiros; 83% foram publicadas em revistas internacionais. Identifica os seguintes enfoques de estudos sobre o tema: a) propostas de sistemas de recomendação personalizada baseada na Folksonomia; b) interoperabilidade de metadados semânticos orientados pelos(as) usuários(as); c) estudos exploratórios de interface de repositórios digitais; d) propostas de navegação híbrida em repositórios digitais com base na Folksonomia e em sistemas formais como ontologias. Conclui evidenciando a predominância de pesquisas voltadas para sistemas de recomendação e interoperabilidade de metadados semânticos orientados pelos usuários. Identifica ainda que as pesquisas sobre a temática são pouco exploradas na literatura, sobretudo no contexto nacional, se configurando como um universo de estudo a ser explorado pelos profissionais e pesquisadores da área.ABSTRACTIt studies aspects concerning Folksonomy and the collaborative representation of information in systems such as Digital Repositories. It aims to analyze the national and international scientific production on Folksonomy in Digital Repositories. Specifically aims to: demonstrate the status of scientific productions on this topic; categorize the approaches of studies on the theme and present the trends and perspectives of studies on the theme. Its methodology is bibliographical, exploratory and descriptive research with a quantitative and qualitative approach for the purpose of recovery, analysis and mapping of national and international scientific production on the subject in the CAPES Journal Portal. Finds that 53% of the recovered scientific productions were published in the period from 2010 to 2015 and 47% of the works are distributed in the time interval between 2016 to 2020. It shows that among the retrieved articles, 17% are researches published in Brazilian journals; 83% were published in international journals. It identifies the following focus of studies on the subject: a) proposals for personalized recommendation systems based on Folksonomy; b) interoperability of user-oriented semantic metadata; c) exploratory studies of digital repositories interface; d) proposals for hybrid navigation in digital repositories based on Folksonomy and formal systems such as ontologies. It concludes by highlighting the predominance of research aimed at recommendation systems and user-oriented semantic metadata interoperability. Also identifies that research on the subject is little explored in the literature, especially in the national conext, configuring itself as a study universe to be explored by professionals and researchers in the area.

Wikidata Support in the Creation of Rich Semantic Metadata for Historical Archives

The research question this paper aims at answering is the following: In an ontology-driven annotation system, can the information extracted from external resources (namely, Wikidata) provide users with useful suggestions in the characterization of entities used for the annotation of documents from historical archives? The context of the research is the PRiSMHA project, in which the main goal is the development of a proof-of-concept prototype ontology-driven system for semantic metadata generation. The assumption behind this effort is that an effective access to historical archives needs a rich semantic knowledge, relying on a domain ontology, that describes the content of archival resources. In the paper, we present a new feature of the annotation system: when characterizing a new entity (e.g., a person), some properties describing it are automatically pre-filled in, and more complex semantic representations (e.g., events the entity is involved in) are suggested; both kinds of suggestions are based on information retrieved from Wikidata. In the paper, we describe the automatic algorithm devised to support the definition of the mappings between the Wikidata semantic model and the PRiSMHA ontology, as well as the process used to extract information from Wikidata and to generate suggestions based on the defined mappings. Finally, we discuss the results of a qualitative evaluation of the suggestions, which provides a positive answer to the initial research question and indicates possible improvements.

Contrasting Ontology Modeling with Correlation Rules for Delivery Applications

With the increasing importance of knowledge management, variant management and the ever-growing quantity of data, ontologies emerged as a form of knowledge representation, especially in the field of technical communication for modelling metadata and to create correlations between them. In the area of delivery applications, the deliverable information objects receive a certain intelligence by semantic metadata. It is expected, that ontologies offer a higher level of intelligence which could lead to an improvement in classification, connection and delivery possibilities of content. On the contrary, creating those complex ontologies requires a time-consuming effort. Thus, the question arises, whether their use offers a decisive added benefit or if alternatives, such as untyped correlations, should be preferred. In that case, the concept of Semantic Correlation Rules can offer an opportunity to derive advantages from ontologies: By defining which classifications are connected to others, it is possible to present content tailored to user-specific information requirements. By developing use cases, we aim to evaluate the required level of intelligence of the metadata resulting from its modeling method to achieve this goal.

A Review of Geospatial Semantic Information Modeling and Elicitation Approaches

The present paper provides a review of two research topics that are central to geospatial semantics: information modeling and elicitation. The first topic deals with the development of ontologies at different levels of generality and formality, tailored to various needs and uses. The second topic involves a set of processes that aim to draw out latent knowledge from unstructured or semi-structured content: semantic-based extraction, enrichment, search, and analysis. These processes focus on eliciting a structured representation of information in various forms such as: semantic metadata, links to ontology concepts, a collection of topics, etc. The paper reviews the progress made over the last five years in these two very active areas of research. It discusses the problems and the challenges faced, highlights the types of semantic information formalized and extracted, as well as the methodologies and tools used, and identifies directions for future research.

Extending intelligent content delivery in technical communication by semantics: microdocuments and content services

We address and develop a new concept for the dynamic delivery of topic-based content created within the domain of technical communication. Corresponding content management environments introduced within the last decades, focused so far on semantically structured and mostly XML-based information models and, more recently, on semantic metadata using taxonomies leading together to concepts of so-called intelligent content. Latest developments attempt to extend these concepts with additional explicit semantic approaches modelled and implemented, for example, by using ontologies and related technologies. In this article, we propose how content users might benefit from these semantic concepts by the delivery of sets of logically connected topics, which can be described as microdocuments (“microDocs”). This generic approach of topic assemblies might also play a role in the provisioning of content by web-services being integrated into different types of content processing and content delivery applications.