A MOD(ern) perspective on literature curation

Curation of biological data is a multi-faceted task whose goal is to create a structured, comprehensive, integrated, and accurate resource of current biological knowledge. These structured data facilitate the work of the scientific community by providing knowledge about genes or genomes and by generating validated connections between the data that yield new information and stimulate new research approaches. For the model organism databases (MODs), an important source of data is research publications. Every published paper containing experimental information about a particular model organism is a candidate for curation. All such papers are examined carefully by curators for relevant information. Here, four curators from different MODs describe the literature curation process and highlight approaches taken by the four MODs to address: (1) the decision process by which papers are selected, and (2) the identification and prioritization of the data contained in the paper. We will highlight some of the challenges that MOD biocurators face, and point to ways in which researchers and publishers can support the work of biocurators and the value of such support

A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework

The breadth of information resources available to researchers on the Internet continues to expand, particularly in light of recently implemented data-sharing policies required by funding agencies. However, the nature of dense, multifaceted neuroscience data and the design of contemporary search engine systems makes efficient, reliable and relevant discovery of such information a significant challenge. This challenge is specifically pertinent for online databases, whose dynamic content is ‘hidden’ from search engines. The Neuroscience Information Framework (NIF; http://www.neuinfo.org) was funded by the NIH Blueprint for Neuroscience Research to address the problem of finding and utilizing neuroscience-relevant resources such as software tools, data sets, experimental animals and antibodies across the Internet. From the outset, NIF sought to provide an accounting of available resources, whereas developing technical solutions to finding, accessing and utilizing them. The curators therefore, are tasked with identifying and registering resources, examining data, writing configuration files to index and display data and keeping the contents current. In the initial phases of the project, all aspects of the registration and curation processes were manual. However, as the number of resources grew, manual curation became impractical. This report describes our experiences and successes with developing automated resource discovery and semiautomated type characterization with text-mining scripts that facilitate curation team efforts to discover, integrate and display new content. We also describe the DISCO framework, a suite of automated web services that significantly reduce manual curation efforts to periodically check for resource updates. Lastly, we discuss DOMEO, a semi-automated annotation tool that improves the discovery and curation of resources that are not necessarily website-based (i.e. reagents, software tools). Although the ultimate goal of automation was to reduce the workload of the curators, it has resulted in valuable analytic by-products that address accessibility, use and citation of resources that can now be shared with resource owners and the larger scientific community

A Framework to Support Digital Humanities and Cultural Heritage Studies Research

Developments in information and communication technologies and their repercussions for how cultural heritage is preserved, used and produced are the subject of several research and innovation efforts in Europe. Advanced digital technologies create new opportunities for cultural heritage to drive innovation. Digital humanities are an important domain for cultural heritage research in Europe and beyond. Digital tools and methods can be used in innovative ways in cultural heritage research. The research and innovation efforts and framework of digital humanities, and cultural heritage as one of its research fields, are influenced by EU policies and legislation. This article describes the existing policy initiatives, practices and related legal setting as framework conditions for digital humanities and cultural heritage research and innovation in Europe – focusing on urban history applications in the age of digital libraries. This is a multifaceted study of the state of the art in policies, legislation and standards – using a survey with 1000 participants, literature surveys on copyrights and policies

Natural Language Processing in-and-for Design Research

We review the scholarly contributions that utilise Natural Language Processing (NLP) methods to support the design process. Using a heuristic approach, we collected 223 articles published in 32 journals and within the period 1991-present. We present state-of-the-art NLP in-and-for design research by reviewing these articles according to the type of natural language text sources: internal reports, design concepts, discourse transcripts, technical publications, consumer opinions, and others. Upon summarizing and identifying the gaps in these contributions, we utilise an existing design innovation framework to identify the applications that are currently being supported by NLP. We then propose a few methodological and theoretical directions for future NLP in-and-for design research

A prior case study of natural language processing on different domain

In the present state of digital world, computer machine do not understand the human’s ordinary language. This is the great barrier between humans and digital systems. Hence, researchers found an advanced technology that provides information to the users from the digital machine. However, natural language processing (i.e. NLP) is a branch of AI that has significant implication on the ways that computer machine and humans can interact. NLP has become an essential technology in bridging the communication gap between humans and digital data. Thus, this study provides the necessity of the NLP in the current computing world along with different approaches and their applications. It also, highlights the key challenges in the development of new NLP model

frances : cloud-based historical text mining with deep learning and parallel processing

frances is an advanced cloud-based text mining digital platform that leverages information extraction, knowledge graphs, natural language processing (NLP), deep learning, and parallel processing techniques. It has been specifically designed to unlock the full potential of historical digital textual collections, such as those from the National Library of Scotland, offering cloud-based capabilities and extended support for complex NLP analyses and data visualizations. frances enables realtime recurrent operational text mining and provides robust capabilities for temporal analysis, accompanied by automatic visualizations for easy result inspection. In this paper, we present the motivation behind the development of frances, emphasizing its innovative design and novel implementation aspects. We also outline future development directions. Additionally, we evaluate the platform through two comprehensive case studies in history and publishing history. Feedback from participants in these studies demonstrates that frances accelerates their work and facilitates rapid testing and dissemination of ideas.Postprin

Hybrid human-AI driven open personalized education

Attaining those skills that match labor market demand is getting increasingly complicated as prerequisite knowledge, skills, and abilities are evolving dynamically through an uncontrollable and seemingly unpredictable process. Furthermore, people's interests in gaining knowledge pertaining to their personal life (e.g., hobbies and life-hacks) are also increasing dramatically in recent decades. In this situation, anticipating and addressing the learning needs are fundamental challenges to twenty-first century education. The need for such technologies has escalated due to the COVID-19 pandemic, where online education became a key player in all types of training programs. The burgeoning availability of data, not only on the demand side but also on the supply side (in the form of open/free educational resources) coupled with smart technologies, may provide a fertile ground for addressing this challenge. Therefore, this thesis aims to contribute to the literature about the utilization of (open and free-online) educational resources toward goal-driven personalized informal learning, by developing a novel Human-AI based system, called eDoer. In this thesis, we discuss all the new knowledge that was created in order to complete the system development, which includes 1) prototype development and qualitative user validation, 2) decomposing the preliminary requirements into meaningful components, 3) implementation and validation of each component, and 4) a final requirement analysis followed by combining the implemented components in order develop and validate the planned system (eDoer). All in all, our proposed system 1) derives the skill requirements for a wide range of occupations (as skills and jobs are typical goals in informal learning) through an analysis of online job vacancy announcements, 2) decomposes skills into learning topics, 3) collects a variety of open/free online educational resources that address those topics, 4) checks the quality of those resources and topic relevance using our developed intelligent prediction models, 5) helps learners to set their learning goals, 6) recommends personalized learning pathways and learning content based on individual learning goals, and 7) provides assessment services for learners to monitor their progress towards their desired learning objectives. Accordingly, we created a learning dashboard focusing on three Data Science related jobs and conducted an initial validation of eDoer through a randomized experiment. Controlling for the effects of prior knowledge as assessed by the pretest, the randomized experiment provided tentative support for the hypothesis that learners who engaged with personal eDoer recommendations attain higher scores on the posttest than those who did not. The hypothesis that learners who received personalized content in terms of format, length, level of detail, and content type, would achieve higher scores than those receiving non-personalized content was not supported as a statistically significant result

Structuring research methods and data with the research object model:genomics workflows as a case study

Background: One of the main challenges for biomedical research lies in the computer-assisted integrative study of large and increasingly complex combinations of data in order to understand molecular mechanisms. The preservation of the materials and methods of such computational experiments with clear annotations is essential for understanding an experiment, and this is increasingly recognized in the bioinformatics community. Our assumption is that offering means of digital, structured aggregation and annotation of the objects of an experiment will provide necessary meta-data for a scientist to understand and recreate the results of an experiment. To support this we explored a model for the semantic description of a workflow-centric Research Object (RO), where an RO is defined as a resource that aggregates other resources, e. g., datasets, software, spreadsheets, text, etc. We applied this model to a case study where we analysed human metabolite variation by workflows. Results: We present the application of the workflow-centric RO model for our bioinformatics case study. Three workflows were produced following recently defined Best Practices for workflow design. By modelling the experiment as an RO, we were able to automatically query the experiment and answer questions such as "which particular data was input to a particular workflow to test a particular hypothesis?", and "which particular conclusions were drawn from a particular workflow?". Conclusions: Applying a workflow-centric RO model to aggregate and annotate the resources used in a bioinformatics experiment, allowed us to retrieve the conclusions of the experiment in the context of the driving hypothesis, the executed workflows and their input data. The RO model is an extendable reference model that can be used by other systems as well. Availability: The Research Object is available at http://www.myexperiment.org/packs/428 The Wf4Ever Research Object Model is available at http://wf4ever.github.io/r

An Ontology based Text-to-Picture Multimedia m-Learning System

Multimedia Text-to-Picture is the process of building mental representation from words associated with images. From the research aspect, multimedia instructional message items are illustrations of material using words and pictures that are designed to promote user realization. Illustrations can be presented in a static form such as images, symbols, icons, figures, tables, charts, and maps; or in a dynamic form such as animation, or video clips. Due to the intuitiveness and vividness of visual illustration, many text to picture systems have been proposed in the literature like, Word2Image, Chat with Illustrations, and many others as discussed in the literature review chapter of this thesis. However, we found that some common limitations exist in these systems, especially for the presented images. In fact, the retrieved materials are not fully suitable for educational purposes. Many of them are not context-based and didn’t take into consideration the need of learners (i.e., general purpose images). Manually finding the required pedagogic images to illustrate educational content for learners is inefficient and requires huge efforts, which is a very challenging task. In addition, the available learning systems that mine text based on keywords or sentences selection provide incomplete pedagogic illustrations. This is because words and their semantically related terms are not considered during the process of finding illustrations. In this dissertation, we propose new approaches based on the semantic conceptual graph and semantically distributed weights to mine optimal illustrations that match Arabic text in the children’s story domain. We combine these approaches with best keywords and sentences selection algorithms, in order to improve the retrieval of images matching the Arabic text. Our findings show significant improvements in modelling Arabic vocabulary with the most meaningful images and best coverage of the domain in discourse. We also develop a mobile Text-to-Picture System that has two novel features, which are (1) a conceptual graph visualization (CGV) and (2) a visual illustrative assessment. The CGV shows the relationship between terms associated with a picture. It enables the learners to discover the semantic links between Arabic terms and improve their understanding of Arabic vocabulary. The assessment component allows the instructor to automatically follow up the performance of learners. Our experiments demonstrate the efficiency of our multimedia text-to-picture system in enhancing the learners’ knowledge and boost their comprehension of Arabic vocabulary