A systematic review on literature-based discovery workflow

Classification of Covid-19 misinformation on social media based on neuro-fuzzy and neural network: A systematic review

The spread of Covid-19 misinformation on social media had significant real-world consequences, and it raised fears among internet users since the pandemic has begun. Researchers from all over the world have shown an interest in developing deception classification methods to reduce the issue. Despite numerous obstacles that can thwart the efforts, the researchers aim to create an automated, stable, accurate, and effective mechanism for misinformation classification. In this paper, a systematic literature review is conducted to analyse the state-of-the-art related to the classification of misinformation on social media. IEEE Xplore, SpringerLink, ScienceDirect, Scopus, Taylor & Francis, Wiley, Google Scholar are used as databases to find relevant papers since 2018-2021. Firstly, the study begins by reviewing the history of the issues surrounding Covid-19 misinformation and its effects on social media users. Secondly, various neuro-fuzzy and neural network classification methods are identified. Thirdly, the strength, limitations, and challenges of neuro-fuzzy and neural network approaches are verified for the classification misinformation specially in case of Covid-19. Finally, the most efficient hybrid method of neuro-fuzzy and neural networks in terms of performance accuracy is discovered. This study is wrapped up by suggesting a hybrid ANFIS-DNN model for improving Covid-19 misinformation classification. The results of this study can be served as a roadmap for future research on misinformation classification.

Network Analysis of Inflammatory Bowel Disease Research: Towards the Interactome

BACKGROUND AND AIMS

Modern views accept that inflammatory bowel diseases [IBD] emerge from complex interactions among the multiple components of a biological network known as the 'IBD interactome'. These diverse components belong to different functional levels including cells, molecules, genes and biological processes. This diversity can make it difficult to integrate available empirical information from human patients into a collective view of aetiopathogenesis, a necessary step to understand the interactome. Herein, we quantitatively analyse how the representativeness of components involved in human IBD and their relationships ha ve changed over time.

METHODS

A bibliographic search in PubMed retrieved 25 971 abstracts of experimental studies on IBD in humans, published between 1990 and 2020. Abstracts were scanned automatically for 1218 IBD interactome components proposed in recent reviews. The resulting databases are freely available and were visualized as networks indicating the frequency at which different components are referenced together within each abstract.

RESULTS

As expected, over time there was an increase in components added to the IBD network and heightened connectivity within and across functional levels. However, certain components were consistently studied together, forming preserved motifs in the networks. These overrepresented and highly linked components reflect main 'hypotheses' in IBD research in humans. Interestingly, 82% of the components cited in reviews were absent or showed low frequency, suggesting that many aspects of the proposed IBD interactome still have weak experimental support in humans.

CONCLUSIONS

A reductionist and fragmented approach to the study of IBD has prevailed in previous decades, highlighting the importance of transitioning towards a more integrated interactome framework.

Non-Specific Low Back Pain, Dietary Salt Intake, and Posterior Lumbar Subcutaneous Edema

Low back pain is the world’s leading disability, but the etiology of the majority of low back pain is non-specific with no known cause. Moreover, overuse of opioids to treat low back pain is a widespread problem. This paper proposes that non-specific low back pain may be associated with excessive intake of dietary salt, potentially mediated by posterior lumbar subcutaneous edema. In addition to pain, symptoms of edema include swelling, tightness, and stiff joints, which are common complaints of people with low back pain, along with restricted lumbar range of motion and impaired mobility. Many global populations consume excess sodium chloride, which can lead to fluid overload in hypervolemia, and cause swelling and temporary weight gain associated with low back pain. Numerous conditions comorbid with low back pain are also potentially mediated by excessive salt intake, including migraine headache, hypertension, cardiovascular disease, venous thromboembolism, liver disease, respiratory disorders, chronic kidney disease, pregnancy complications, and multiple sclerosis. Novel approaches to identify and prevent the cause of non-specific low back pain have potential to reduce disability worldwide by reducing low back pain prevalence. More research is needed to confirm the involvement of dietary salt and posterior lumbar subcutaneous edema in non-specific low back pain.

Literature Mining of Disease Associated Noncoding RNA in the Omics Era

Noncoding RNAs (ncRNA) are transcripts without protein-coding potential that play fundamental regulatory roles in diverse cellular processes and diseases. The application of deep sequencing experiments in ncRNA research have generated massive omics datasets, which require rapid examination, interpretation and validation based on exiting knowledge resources. Thus, text-mining methods have been increasingly adapted for automatic extraction of relations between an ncRNA and its target or a disease condition from biomedical literature. These bioinformatics tools can also assist in more complex research, such as database curation of candidate ncRNAs and hypothesis generation with respect to pathophysiological mechanisms. In this concise review, we first introduced basic concepts and workflow of literature mining systems. Then, we compared available bioinformatics tools tailored for ncRNA studies, including the tasks, applicability, and limitations. Their powerful utilities and flexibility are demonstrated by examples in a variety of diseases, such as Alzheimer’s disease, atherosclerosis and cancers. Finally, we outlined several challenges from the viewpoints of both system developers and end users. We concluded that the application of text-mining techniques will booster disease-associated ncRNA discoveries in the biomedical literature and enable integrative biology in the current omics era.

Computational Literature-based Discovery for Natural Products Research: Current State and Future Prospects

Literature-based discovery (LBD) mines existing literature in order to generate new hypotheses by finding links between previously disconnected pieces of knowledge. Although automated LBD systems are becoming widespread and indispensable in a wide variety of knowledge domains, little has been done to introduce LBD to the field of natural products research. Despite growing knowledge in the natural product domain, most of the accumulated information is found in detached data pools. LBD can facilitate better contextualization and exploitation of this wealth of data, for example by formulating new hypotheses for natural product research, especially in the context of drug discovery and development. Moreover, automated LBD systems promise to accelerate the currently tedious and expensive process of lead identification, optimization, and development. Focusing on natural product research, we briefly reflect the development of automated LBD and summarize its methods and principal data sources. In a thorough review of published use cases of LBD in the biomedical domain, we highlight the immense potential of this data mining approach for natural product research, especially in context with drug discovery or repurposing, mode of action, as well as drug or substance interactions. Most of the 91 natural product-related discoveries in our sample of reported use cases of LBD were addressed at a computer science audience. Therefore, it is the wider goal of this review to introduce automated LBD to researchers who work with natural products and to facilitate the dialogue between this community and the developers of automated LBD systems.

Combining Literature Mining and Machine Learning for Predicting Biomedical Discoveries

The major outcomes and insights of scientific research and clinical study end up in the form of publication or clinical record in an unstructured text format. Due to advancements in biomedical research, the growth of published literature is getting tremendous large in recent years. The scientists and clinical researchers are facing a big challenge to stay current with the knowledge and to extract hidden information from this sheer quantity of millions of published biomedical literature. The potential one-stop automated solution to this problem is biomedical literature mining. One of the long-standing goals in biology is to discover the disease-causing genes and their specific roles in personalized precision medicine and drug repurposing. However, the empirical approaches and clinical affirmation are expensive and time-consuming. In silico approach using text mining to identify the disease causing genes can contribute towards biomarker discovery. This chapter presents a protocol on combining literature mining and machine learning for predicting biomedical discoveries with a special emphasis on gene-disease relation based discovery. The protocol is presented as a literature based discovery (LBD) pipeline for gene-disease based discovery. The protocol includes our web based tools: (1) DNER (Disease Named Entity Recognizer) for disease entity recognition, (2) BCCNER (Bidirectional, Contextual clues Named Entity Tagger) for gene/protein entity recognition, (3) DisGeReExT (Disease-Gene Relation Extractor) for statistically validated results and visualization, and (4) a newly introduced deep learning based method for association discovery. Our proposed deep learning based method can be generalized and applied to other important biomedical discoveries focusing on entities such as drug/chemical, or miRNA.

Understanding the Usability of a Literature-Based Discovery System Among Clinical Researchers in Sarawak, Malaysia

The rapid increase in scientific publications makes it difficult for researchers to keep up with the latest literature and to explore new research directions. The literature-based discovery (LBD) systems aim to resolve this issue by bridging literatures from disparate fields to assist researchers in knowledge discovery and the formulation and testing of research hypotheses. Previous studies have focused mainly on evaluating the efficacy of LBD systems by replicating historical LBD events. The usability of LBD systems has been under-researched, which partly explains the low adoption of the systems. This paper presents a survey study that evaluates the usability of a LBD system for knowledge discovery and hypothesis refinement, and also investigates factors affecting its adoption among biomedical researchers in Sarawak, Malaysia. The findings suggest that the adoption of the LBD system is related to their perceived usefulness and perceived difficulty in interacting with the user interface features of the system.

MeSH and text-word search strategies: precision, recall, and their implications for library instruction

OBJECTIVE

This study compared the recall and precision of MeSH-term versus text-word searching to better understand psychosocial MeSH terms and to provide guidance on whether to include both strategies in an information literacy session or how much time should be spent on teaching each search strategy.

METHODS

Using the relevant recall method, a total of 3,162 resources were considered and evaluated to form a gold standard set of 1,521 relevant resources. We compared resources discussing psychosocial aspects of children and adolescents living with type 1 diabetes using two search strategies: text-word strategy versus MeSH-term strategy. The frequency of MeSH terms, the MeSH hierarchy, and elements of each search strategy were also examined.

RESULTS

Using the 1,521 relevant articles, we found that the text-word search strategy had 54% recall, while the MeSH-term strategy had 75% recall. Also, the precision of the text-word strategy was 34.4%, while the precision of the MeSH-term strategy was 47.7%. Therefore, the MeSH-term search strategy yielded both greater recall and greater precision. The MeSH strategy was also more complicated in design and usage than the text-word strategy.

CONCLUSIONS

This study demonstrates the effectiveness of text-word and MeSH search strategies on precision and recall. The combination of text-word and MeSH strategies is recommended to achieve the most comprehensive results. These results support the idea that MeSH or a similar controlled vocabulary should be taught to experienced and knowledgeable students and practitioners who require a myriad of resources for their literature searches.

Exploration of Shared Themes Between Food Security and Internet of Things Research Through Literature-Based Discovery

This paper applied a literature-based discovery methodology utilizing citation networks and text mining in order to extract and represent shared terminologies found in disjoint academic literature on food security and the Internet of Things. The topic of food security includes research on improvements in nutrition, sustainable agriculture, and a plurality of other social challenges, while the Internet of Things refers to a collection of technologies from which solutions can be drawn. Academic articles on both topics were classified into subclusters, and their text contents were compared against each other to find shared terms. These terms formed a network from which clusters of related keywords could be identified, potentially easing the exploration of common themes. Thirteen transversal themes, including blockchain, healthcare, and air quality, were found. This method can be applied by policymakers and other stakeholders to understand how a given technology could contribute to solving a pressing social issue.

Defragmenting Research Areas with Knowledge Visualization and Visual Text Analytics

The increasing specialization of science is motivating the fragmentation of traditional and well-established research areas into interdisciplinary communities of practice that focus on cooperation between experts to solve problems in a wide range of domains. This is the case of problem-driven visualization research (PDVR), in which groups of scholars use visualization techniques in different application domains such as the digital humanities, bioinformatics, sports science, or computer security. In this paper, we employ the findings obtained during the development of a novel visual text analytics tool we built in previous studies, GlassViz, to automatically detect interesting knowledge associations and groups of common interests between these communities of practice. Our proposed method relies on the statistical modeling of author-assigned keywords to make its findings, which are demonstrated in two use cases. The results show that it is possible to propose interactive, semisupervised visual approaches that aim at defragmenting a body of research using text-based, automatic literature analysis methods.

Reviewing Research Trends—A Scientometric Approach Using Gunshot Residue (GSR) Literature as an Example

The ability to manage, distil and disseminate the significant amount of information that is available from published literature is fast becoming a core and critical skill across all research domains, including that of forensic science. In this study, a simplified scientometric approach has been applied to available literature on gunshot residue (GSR) as a test evidence type aiming to evaluate publication trends and explore the interconnectivity between authors. A total of 731 publications were retrieved using the search engine ‘Scopus’ and come from 1589 known authors, of whom 401 contributed to more than one research output on this subject. Out of the total number of publications, only 35 (4.8%) were found to be Open Access (OA). The Compound Annual Growth Rate (CAGR) for years 2006 and 2016 reveals a much higher growth in publications relating to GSR (8.0%) than the benchmark annual growth rate of 3.9%. The distribution of a broad spectrum of keywords generated from the publications confirms a historical trend, in particular regarding the use of analytical techniques, in the study of gunshot residue. The results inform how relevant information extracted from a bibliometric search can be used to explore, analyse and define new research areas.

Connecting the Dots: Hypotheses Generation by Leveraging Semantic Shifts

Literature-based Discovery (LBD) (a.k.a. Hypotheses Generation) is a systematic knowledge discovery process that elicit novel inferences about previously unknown scientific knowledge by rationally connecting complementary and non-interactive literature. Prompt identification of such novel knowledge is beneficial not only for researchers but also for various other stakeholders such as universities, funding bodies and academic publishers. Almost all the prior LBD research suffer from two major limitations. Firstly, the over-reliance of domain-dependent resources which restrict the models’ applicability to certain domains/problems. In this regard, we propose a generalisable LBD model that supports both cross-domain and cross-lingual knowledge discovery. The second persistent research deficiency is the mere focus of static snapshot of the corpus (i.e. ignoring the temporal evolution of topics) to detect the new knowledge. However, the knowledge in scientific literature changes dynamically and thus relying merely on static snapshot limits the model’s ability in capturing semantically meaningful connections. As a result, we propose a novel temporal model that captures semantic change of topics using diachronic word embeddings to unravel more accurate connections. The model was evaluated using the largest available literature repository to demonstrate the efficiency of the proposed cues towards recommending novel knowledge.