Literature-based Discovery Approach Research Articles

Automated extraction of synthesis parameters of pulsed laser-deposited materials from scientific literature

An efficient data-driven literature-based discovery approach is utilized, that is capable of extracting knowledge from materials science-related text, related to Pulsed Laser Deposition (PLD), aiming to extract various processing parameters that are critical during the PLD process.

A Knowledge Graph of Mechanistic Associations Between COVID-19, Diabetes Mellitus, and Chronic Kidney Disease.

We present an automated knowledge synthesis and discovery framework to analyze published literature to identify and represent underlying mechanistic associations that aggravate chronic conditions due to COVID-19. Our literature-based discovery approach integrates text mining, knowledge graphs and medical ontologies to discover hidden and previously unknown pathophysiologic relations, dispersed across multiple public literature databases, between COVID-19 and chronic disease mechanisms. We applied our approach to discover mechanistic associations between COVID-19 and chronic conditions-i.e. diabetes mellitus and chronic kidney disease-to understand the long-term impact of COVID-19 on patients with chronic diseases. We found several gene-disease associations that could help identify mechanisms driving poor outcomes for COVID-19 patients with underlying conditions.

Literature-based discovery approaches for evidence-based healthcare: a systematic review.

PurposeLiterature-Based Discovery (LBD) is a text mining technique used to generate novel hypotheses from vast amounts of literature sources, by identifying links between concepts from disparate sources. One of the main areas where it has been predominantly applied is the healthcare domain, whereby promising results, in the form of novel hypotheses, have been reported. The purpose of this work was to conduct a systematic literature review of recent publications on LBD in the healthcare domain in order to assess the trends in the approaches used and to identify issues and challenges for such systems.MethodsThe review was conducted following the principles of the Kitchenham method. The selected studies have been scrutinized and the derived findings have been reported following the PRISMA guidelines.ResultsThe review results reveal useful information regarding the application areas, the data sources considered, the approaches used, the performance in terms of accuracy and reliability and future research challenges. The results of this review will be beneficial to LBD researchers and other stakeholders in the healthcare domain, by providing them with useful insights on the approaches to adopt, data sources to consider, evaluation model to use and challenges to reflect on.ConclusionThe synthesis of the results of this work has shed light on recent issues and challenges that drive new LBD models and provides avenues for their application in other diverse areas in the healthcare domain. To the best of our knowledge, no such recent review has been conducted.

A Knowledge Graph of Mechanistic Associations Between COVID-19, Diabetes Mellitus and Kidney Diseases.

This paper proposes an automated knowledge synthesis and discovery framework to analyze published literature to identify and represent underlying mechanistic associations that aggravate chronic conditions due to COVID-19. We present a literature-based discovery approach that integrates text mining, knowledge graphs and ontologies to discover semantic associations between COVID-19 and chronic disease concepts that were represented as a complex disease knowledge network that can be queried to extract plausible mechanisms by which COVID-19 may be exacerbated by underlying chronic conditions.

Drug repurposing for COVID-19 via knowledge graph completion

ObjectiveTo discover candidate drugs to repurpose for COVID-19 using literature-derived knowledge and knowledge graph completion methods. MethodsWe propose a novel, integrative, and neural network-based literature-based discovery (LBD) approach to identify drug candidates from PubMed and other COVID-19-focused research literature. Our approach relies on semantic triples extracted using SemRep (via SemMedDB). We identified an informative and accurate subset of semantic triples using filtering rules and an accuracy classifier developed on a BERT variant. We used this subset to construct a knowledge graph, and applied five state-of-the-art, neural knowledge graph completion algorithms (i.e., TransE, RotatE, DistMult, ComplEx, and STELP) to predict drug repurposing candidates. The models were trained and assessed using a time slicing approach and the predicted drugs were compared with a list of drugs reported in the literature and evaluated in clinical trials. These models were complemented by a discovery pattern-based approach. ResultsAccuracy classifier based on PubMedBERT achieved the best performance (F1 = 0.854) in identifying accurate semantic predications. Among five knowledge graph completion models, TransE outperformed others (MR = 0.923, Hits@1 = 0.417). Some known drugs linked to COVID-19 in the literature were identified, as well as others that have not yet been studied. Discovery patterns enabled identification of additional candidate drugs and generation of plausible hypotheses regarding the links between the candidate drugs and COVID-19. Among them, five highly ranked and novel drugs (i.e., paclitaxel, SB 203580, alpha 2-antiplasmin, metoclopramide, and oxymatrine) and the mechanistic explanations for their potential use are further discussed. ConclusionWe showed that a LBD approach can be feasible not only for discovering drug candidates for COVID-19, but also for generating mechanistic explanations. Our approach can be generalized to other diseases as well as to other clinical questions. Source code and data are available at https://github.com/kilicogluh/lbd-covid.

Coronaviruses and people with intellectual disability: an exploratory data analysis.

BackgroundCorona virus disease 2019 (COVID‐19) has been announced as a new coronavirus disease by the World Health Organization. At the time of writing this article (April 2020), the world is drastically influenced by the COVID‐19. Recently, the COVID‐19 Open Research Dataset (CORD‐19) was published. For researchers on ID such as ourselves, it is of key interest to learn whether this open research dataset may be used to investigate the virus and its consequences for people with an ID.MethodsFrom CORD‐19, we identified full‐text articles containing terms related to the ID care and applied a text mining technique, specifically the term frequency–inverse document frequency analysis in combination with K‐means clustering.ResultsTwo hundred fifty‐nine articles contained one or more of our specified terms related to ID. We were able to cluster these articles related to ID into five clusters on different topics, namely: mental health, viral diseases, diagnoses and treatments, maternal care and paediatrics, and genetics.ConclusionThe CORD‐19 open research dataset consists of valuable information about not only COVID‐19 disease but also ID and the relationship between them. We suggest researchers investigate literature‐based discovery approaches on the CORD‐19 and develop a new dataset that addresses the intersection of these two fields for further research.

A survey on literature based discovery approaches in biomedical domain.

Literature Based Discovery (LBD) refers to the problem of inferring new and interesting knowledge by logically connecting independent fragments of information units through explicit or implicit means. This area of research, which incorporates techniques from Natural Language Processing (NLP), Information Retrieval and Artificial Intelligence, has significant potential to reduce discovery time in biomedical research fields. Formally introduced in 1986, LBD has grown to be a significant and a core task for text mining practitioners in the biomedical domain. Together with its inter-disciplinary nature, this has led researchers across domains to contribute in advancing this field of study. This survey attempts to consolidate and present the evolution of techniques in this area. We cover a variety of techniques and provide a detailed description of the problem setting, the intuition, the advantages and limitations of various influential papers. We also list the current bottlenecks in this field and provide a general direction of research activities for the future. In an effort to be comprehensive and for ease of reference for off-the-shelf users, we also list many publicly available tools for LBD. We hope this survey will act as a guide to both academic and industry (bio)-informaticians, introduce the various methodologies currently employed and also the challenges yet to be tackled.

Emerging approaches in literature-based discovery: techniques and performance review

AbstractLiterature-based discovery systems aim at discovering valuable latent connections between previously disparate research areas. This is achieved by analyzing the contents of their respective literatures with the help of various intelligent computational techniques. In this paper, we review the progress of literature-based discovery research, focusing on understanding their technical features and evaluating their performance. The present literature-based discovery techniques can be divided into two general approaches: the traditional approach and the emerging approach. The traditional approach, which dominate the current research landscape, comprises mainly of techniques that rely on utilizing lexical statistics, knowledge-based and visualization methods in order to address literature-based discovery problems. On the other hand, we have also observed the births of new trends and unprecedented paradigm shifts among the recently emerging literature-based discovery approach. These trends are likely to shape the future trajectory of the next generation literature-based discovery systems.

Reducing carbon footprint of facilities using a facility management approach

Purpose The purpose of this paper is to emphasize the importance of a life cycle approach in facilities management practices to reduce the carbon footprint of built facilities. A model to holistic life cycle energy and carbon reduction is also proposed. Design/methodology/approach A literature-based discovery approach was applied to collect, analyze and synthesize the results of published case studies from around the globe. The energy use results of 95 published case studies were analyzed to derive conclusions. Findings A comparison of energy-efficient and conventional facilities revealed that decreasing operating energy may increase the embodied energy components. Additionally, the analysis of 95 commercial buildings indicated that nearly 10 per cent of the total US carbon emissions was influenced by facilities management practices. Research limitations/implications The results were derived from case studies that belonged to various locations across the globe and included facilities constructed with a variety of materials. Practical implications The proposed approach to holistic carbon footprint reduction can guide facility management research and practice to make meaningful contributions to the efforts for creating a sustainable built environment. Originality/value This paper quantifies the extent to which a facilities management professional can contribute to the global efforts of reducing carbon emission.

Systematic analysis of the p53-related microRNAs in breast cancer revealing their essential roles in the cell cycle.

Numerous miRNAs have been found to be involved in the regulation of the p53 signaling pathway. Conversely, p53 regulates the transcription or processing of microRNAs (miRNAs). Given that complexities in the association between p53 and miRNAs exist, and due to the rapidly increasing amount of literature regarding the interactions between p53 and miRNAs, the present study systematically analyzed the associations between miRNAs and p53 in breast cancer using a literature-based discovery approach, natural language processing. A total of 22 miRNAs were found to be associated with p53. Next, three popular online tools (PicTar, miRanda and TargetScan) were used to predict the targets of each miRNA, and certain targets were validated by experiments. Gene Ontology annotation and network analysis demonstrated that the majority of the targets of the p53-related miRNAs were enriched in the cell cycle process. These results suggest that, in addition to regulating the transcription of cell cycle-related genes, p53 also indirectly modulates the cell cycle via miRNAs.

Exploring relation types for literature-based discovery.

Objective Literature-based discovery (LBD) aims to identify “hidden knowledge” in the medical literature by: (1) analyzing documents to identify pairs of explicitly related concepts (terms), then (2) hypothesizing novel relations between pairs of unrelated concepts that are implicitly related via a shared concept to which both are explicitly related. Many LBD approaches use simple techniques to identify semantically weak relations between concepts, for example, document co-occurrence. These generate huge numbers of hypotheses, difficult for humans to assess. More complex techniques rely on linguistic analysis, for example, shallow parsing, to identify semantically stronger relations. Such approaches generate fewer hypotheses, but may miss hidden knowledge. The authors investigate this trade-off in detail, comparing techniques for identifying related concepts to discover which are most suitable for LBD. Materials and methods A generic LBD system that can utilize a range of relation types was developed. Experiments were carried out comparing a number of techniques for identifying relations. Two approaches were used for evaluation: replication of existing discoveries and the “time slicing” approach.1 Results Previous LBD discoveries could be replicated using relations based either on document co-occurrence or linguistic analysis. Using relations based on linguistic analysis generated many fewer hypotheses, but a significantly greater proportion of them were candidates for hidden knowledge. Discussion and Conclusion The use of linguistic analysis-based relations improves accuracy of LBD without overly damaging coverage. LBD systems often generate huge numbers of hypotheses, which are infeasible to manually review. Improving their accuracy has the potential to make these systems significantly more usable.

Finding linkage between technology and social issue: A Literature Based Discovery approach

This paper investigates Literature Based Discovery (LBD) approach to reveal linkages between technology and social issue to elucidate plausible contribution of science and technology for solving social issues. Robotics and gerontology were selected as an example in our analysis. The result shows various technological options of robotics contributing to healthcare and well-being of elderly people, mainly in surgery, rehabilitation, and companionship. In addition, we comparatively evaluated effectiveness of semantic similarity measures to extract these linkages from bibliographic database. Our methodology can be utilized as a decision support tool for managers and policy makers to extract and design promising research targets.

Literature-Based Discovery of IFN-γand Vaccine-Mediated Gene Interaction Networks

Interferon-gamma (IFN-γ) regulates various immune responses that are often critical for vaccine-induced protection. In order to annotate the IFN-γ-related gene interaction network from a large amount of IFN-γ research reported in the literature, a literature-based discovery approach was applied with a combination of natural language processing (NLP) and network centrality analysis. The interaction network of human IFN-γ (Gene symbol: IFNG) and its vaccine-specific subnetwork were automatically extracted using abstracts from all articles in PubMed. Four network centrality metrics were further calculated to rank the genes in the constructed networks. The resulting generic IFNG network contains 1060 genes and 26313 interactions among these genes. The vaccine-specific subnetwork contains 102 genes and 154 interactions. Fifty six genes such as TNF, NFKB1, IL2, IL6, and MAPK8 were ranked among the top 25 by at least one of the centrality methods in one or both networks. Gene enrichment analysis indicated that these genes were classified in various immune mechanisms such as response to extracellular stimulus, lymphocyte activation, and regulation of apoptosis. Literature evidence was manually curated for the IFN-γ relatedness of 56 genes and vaccine development relatedness for 52 genes. This study also generated many new hypotheses worth further experimental studies.

Literature-related discovery (LRD): Water purification

Literature-related discovery (LRD) is the linking of two or more literature concepts that have heretofore not been linked (i.e., disjoint), in order to produce novel, interesting, plausible, and intelligible knowledge (i.e., potential discovery). LRD has two main components that differ in their methodological approach to discovery: Literature-based discovery (LBD) produces potential discovery through analysis of the technical literature alone; Literature-assisted discovery (LAD) produces potential discovery through both analysis of the technical literature and use of selected authors of that literature. These authors generate potential discovery as proposers, workshop/panel participants, or in other active roles. The open discovery systems (ODS) component of LRD starts with a problem to be solved, and generates solutions to that problem through potential discovery. We have been using ODS LRD to identify potential treatments or preventative actions for challenging medical problems, among myriad other applications. The previous four papers in this Special Issue describe the application of ODS LRD (specifically, the ODS LBD variant) to Raynaud's Phenomenon (RP), cataracts, Parkinson's Disease (PD), and Multiple Sclerosis (MS). One goal of the present study was to determine whether LRD could be successfully applied (for the first time) to a challenging non-medical technical problem to generate potential discovery. The second goal was to explore the use of both LRD variants (LBD and LAD) to a non-medical technical problem. We selected the problem of water purification (WP) because of universal applicability and sponsor interest. We used LRD to identify purification concepts, technology components and systems that could lead to improved water purification techniques. We accessed many disparate disciplines to identify purification concepts from literatures not normally associated with water purification. We used two LBD approaches, Cluster Filtering and Latent Semantic Indexing (LSI), to search for potential discovery. We generated voluminous amounts of potential discovery, and believe we have only scratched the surface of what is possible. We also ran a short experiment using LAD to identify experts associated with potential discovery concepts, and use their expertise to generate potential discovery for water purification.

Literature-Related Discovery (LRD): Introduction and background

Discovery in science is the generation of novel, interesting, plausible, and intelligible knowledge about the objects of study. Literature-related discovery (LRD) is the linking of two or more literature concepts that have heretofore not been linked (i.e., disjoint), in order to produce novel, interesting, plausible, and intelligible knowledge (i.e., potential discovery). LRD has two main components that differ in their methodological approach to discovery: • Literature-based discovery (LBD) produces potential discovery through analysis of the technical literature alone. • Literature-assisted discovery (LAD) produces potential discovery through both analysis of the technical literature and use of selected authors of that literature. These authors generate potential discovery as proposers, workshop/panel participants, or in other active roles. LRD offers the promise of large amounts of potential discovery, for the following reasons: • the burgeoning technical literature contains a very large pool of technical concepts in myriad technical areas; • researchers spend full time trying to cover the literature in their own research fields and are relatively unfamiliar with research in other especially disparate fields of research; • the large number of technical concepts (and disparate technical concepts) means that many combinations of especially disparate technical concepts exist • by the laws of probability, some of these combinations will produce novel, interesting, plausible, and intelligible knowledge about the objects of study. This Special Issue presents the LRD methodology and voluminous discovery results from five problem areas: four medical (treatments for Parkinson's Disease (PD), Multiple Sclerosis (MS), Raynaud's Phenomenon (RP), and Cataracts) and one non-medical (Water Purification (WP)). In particular, the open discovery systems (ODS) aspect of LRD (start with problem, generate potential solution(s), or vice versa) is addressed, rather than the closed discovery systems (CDS) aspect (start with problem and potential solution(s), generate linking mechanism(s)). In the presentation of potential discovery, a ‘vetting’ process is used that insures both requirements for ODS LBD are met: concepts are linked that have not been linked previously, and novel, interesting, plausible, and intelligible knowledge is produced. The potential discoveries for the PD, MS, Cataracts, and WP problems are the first we have seen reported by this ODS LBD approach, and the numbers of potential discoveries for the ODS LBD benchmark RP problem are almost two orders of magnitude greater than those reported in the open literature by any other ODS LBD researcher who has addressed this benchmark RP problem. The WP problem is the first non-medical technical topic to have been addressed successfully by ODS LBD. In all cases, but especially the medical, we have barely scratched the surface of quantity and quality of potential discovery that could be generated with adequately resourced studies. Based on the many potential discoveries we have obtained, and the promise of far more potential discoveries with adequately resourced studies, we have generated a new paradigm relative to discovery: while the key challenge in traditional discovery is finding a needle-in-a-haystack, the key challenge in ODS LRD (used appropriately) is handling the overwhelming amount of potential discovery available. Additionally, it is our thesis, as the specific ODS LBD studies will demonstrate, that synergistic combinations of our mainly individual potential discoveries are themselves potential discoveries. We demonstrate throughout this Special Issue the synergistic effects of combining a very few potential discoveries or interesting core literature concepts, and believe that these synergistic benefits are operable at larger scales of combination. In the final lessons-learned paper of this Special Issue, we also show that providing evidence for the synergistic benefits of large numbers of potential discoveries or interesting core concepts is very difficult due to the large numbers of potential combinations involved. One variant of the LAD operational mode (identifying disparate discipline recipients for Broad Agency Announcement (BAA) notifications in order to stimulate proposals of new ideas from these disparate disciplines) is presented for WP. Other possible applications of LAD include: 1. Recipients of solicitation announcements (other solicitations similar to BAA, journal Special Issue calls for papers, etc), 2. Participants in Workshops, Advisory Panels, Review Panels, Roadmaps, and War Games, 3. Points of Contact for Field Science Advisors, Foreign Field Offices, Program Officer site visits, and potential transitions.

Literature-related discovery (LRD): Methodology

Literature-related discovery (LRD) is linking two or more literature concepts that have heretofore not been linked (i.e., disjoint), in order to produce novel, interesting, plausible, and intelligible knowledge. LRD has two components: Literature-based discovery (LBD) generates potential discovery through literature analysis alone, whereas literature-assisted discovery (LAD) generates potential discovery through a combination of literature analysis and interactions among selected literature authors. In turn, there are two types of LBD and LAD: open discovery systems (ODS), where one starts with a problem and arrives at a solution, and closed discovery systems (CDS), where one starts with a problem and a solution, then determines the mechanism(s) that links them. The generic methodology for identifying potential discovery candidates through ODS LRD, focusing mainly on its ODS LBD component, is described in this paper. A comprehensive flow chart showing the details of our systematic potential discovery generation process, including the evolution of the flow chart steps through each of the studies performed, is presented. Also shown is a vetting procedure that insures potential discoveries claimed are potential discoveries realized. The semantic filters that replace the numerical filters of other ODS LBD approaches are overviewed. The rationale for addressing the five topics studied (Raynaud's Phenomenon (RP), Cataracts, Parkinson's Disease (PD), Multiple Sclerosis (MS), and Water Purification (WP)) is summarized.

Systematic acceleration of radical discovery and innovation in science and technology

A systematic two-component approach (front-end component, back-end component) to bridging unconnected disciplines and accelerating potentially radical discovery and innovation (based wholly or partially on text mining procedures) is presented. The front-end component has similar objectives to those in the classical literature-based discovery (LBD) approach, although it is different mechanistically and operationally. The front-end component will systematically identify technical disciplines (and their associated leading experts) that are directly or indirectly-related to solving technical problems of high interest. The back-end component is actually a family of back-end techniques, only one of which shares the strictly literature-based analysis of the classical LBD approach. The non-LBD back-end techniques (literature-assisted discovery) make use of the human experts associated with the disparate literatures (disciplines) uncovered in the front-end to generate radical discovery and innovation. Specifically, in the literature-assisted discovery operational mode, these disparate discipline experts could be used as: 1. Recipients of solicitation announcements (BAA, SBIR, MURI, journal Special Issue calls for papers, etc.), 2. Participants in Workshops, Advisory Panels, Review Panels, Roadmaps, and War Games, 3. Points of Contact for Field Science Advisors, Foreign Field Offices, Program Officer site visits, and potential transitions.