DCPC: Drug Candidates for the Prevention of COVID-19 Database

The world immediately studied Coronavirus Disease 2019 (COVID-19) and raced towards finding the cure and developing an effective treatment. An automated approach is needed to discover drug candidates and provide those data to facilitate clinical trials in saving time and only focusing on the candidates which potentially become the cure for COVID-19. We propose the Drug Candidates for the Prevention of COVID-19 (DCPC) Database. DCPC Database provides a list of candidates of potential drugs for the prevention of COVID-19 based on disease-drug associations which are automatically discovered from biomedical literature. DCPC database is an integrative structural database, which involves a chemical database repository, such as PubChem and DrugBank to ensure that drug compound candidates have a standard representation of compounds. The database provides keyword-chosen categories and a determination of minimum supported articles for search, a list of drug candidates in the sorted table followed by the detail for each candidate, and a download feature. The keyword category consists of three keywords, they are Chinese herbal compounds, Indian medicinal plants/and Indian medicinal plants & diabetic treatment herbs. Each candidate links to an article in the biomedical literature and to a page of the compound structure visualization. DCPC is freely available at https://dcpc.brin.go.id/dcpc/. © 2022 IEEE.

Multi-label topic classification for COVID-19 literature annotation: A BioBERT-based feature enhancement approach

With the rapid expansion and exponential growth of biomedical literatures, especially in the current environment of COVID-19 pandemic, it is urgent to explore an effective technology to automatically manage and categorize massive information for biomedical texts. The wide application and powerful performance of BERT have shown promising results in the field of natural language processing. Thus, we first choose the improved pre-trained language models CovidBERT and BioBERT as the basis, from the best performance of which further enhances semantic representation of with extra title information. Finally, a novel feature enhancement method is proposed to exploit and integrate the distribution of label information effectively. The experimental results show that our model achieves an instance-based F1 score, precision and recall of 93.94%, 93.5% and 94.38% in the task of multi-label topic classification from track 5 BioCreative VII. © VDE VERLAG GMBH - Berlin - Offenbach.

DD-RDL: Drug-Disease Relation Discovery and Labeling

Drug repurposing, which is concerned with the study of the effectiveness of existing drugs on new diseases, has been growing in importance in the last few years. One of the core methodologies for drug repurposing is text-mining, where novel biological entity relationships are extracted from existing biomedical literature and publications, whose number skyrocketed in the last couple of years. This paper proposes an NLP approach for drug-disease relation discovery and labeling (DD-RDL), which employs a series of steps to analyze a corpus of s of scientific biomedical research papers. The proposed ML pipeline restructures the free text from a set of words into drug-disease pairs using state-of-the-art text mining methodologies and natural language processing tools. The model’s output is a set of extracted triplets in the form (drug, verb, disease), where each triple describes a relationship between a drug and a disease detected in the corpus. We evaluate the model based on a gold standard dataset for drug-disease relationships, and we demonstrate that it is possible to achieve similar results without requiring a large amount of annotated biological data or predefined semantic rules. Additionally, as an experimental case, we analyze the research papers published as part of the COVID-19 Open Research Dataset (CORD-19) to extract and identify relations between drugs and diseases related to the ongoing pandemic. © 2022, Springer Nature Switzerland AG.

Combining biomedical knowledge graphs and text to improve predictions for drug-target interactions and drug-indications.

Biomedical knowledge is represented in structured databases and published in biomedical literature, and different computational approaches have been developed to exploit each type of information in predictive models. However, the information in structured databases and literature is often complementary. We developed a machine learning method that combines information from literature and databases to predict drug targets and indications. To effectively utilize information in published literature, we integrate knowledge graphs and published literature using named entity recognition and normalization before applying a machine learning model that utilizes the combination of graph and literature. We then use supervised machine learning to show the effects of combining features from biomedical knowledge and published literature on the prediction of drug targets and drug indications. We demonstrate that our approach using datasets for drug-target interactions and drug indications is scalable to large graphs and can be used to improve the ranking of targets and indications by exploiting features from either structure or unstructured information alone.

Repurposing biomedical informaticians for COVID-19.

The COVID-19 pandemic is an unprecedented challenge to the biomedical research community at the intersection of great uncertainty due to the novelty of the virus and extremely high stakes due to the large global death count. The global quarantine shut-downs complicated scientific matters because many laboratories were closed down unless they were actively doing COVID-19 related research, making repurposing of activities difficult for many biomedical researchers. Biomedical informaticians, who have been primarily able to continue their research through remote work and video conferencing, have been able to maintain normal activities. In addition to continuing ongoing studies, there has been great grass roots interest in helping in the fight against COVID-19. In this commentary, we describe several projects that arose from this desire to help, and the lessons that the authors learned along the way. We then offer some insights into how these lessons might be applied to make scientific progress be more efficient in future crisis scenarios.

Identification of Risk Factors and Symptoms of COVID-19: Analysis of Biomedical Literature and Social Media Data.

BACKGROUND: In December 2019, the COVID-19 outbreak started in China and rapidly spread around the world. Lack of a vaccine or optimized intervention raised the importance of characterizing risk factors and symptoms for the early identification and successful treatment of patients with COVID-19. OBJECTIVE: This study aims to investigate and analyze biomedical literature and public social media data to understand the association of risk factors and symptoms with the various outcomes observed in patients with COVID-19. METHODS: Through semantic analysis, we collected 45 retrospective cohort studies, which evaluated 303 clinical and demographic variables across 13 different outcomes of patients with COVID-19, and 84,140 Twitter posts from 1036 COVID-19-positive users. Machine learning tools to extract biomedical information were introduced to identify mentions of uncommon or novel symptoms in tweets. We then examined and compared two data sets to expand our landscape of risk factors and symptoms related to COVID-19. RESULTS: From the biomedical literature, approximately 90% of clinical and demographic variables showed inconsistent associations with COVID-19 outcomes. Consensus analysis identified 72 risk factors that were specifically associated with individual outcomes. From the social media data, 51 symptoms were characterized and analyzed. By comparing social media data with biomedical literature, we identified 25 novel symptoms that were specifically mentioned in tweets but have been not previously well characterized. Furthermore, there were certain combinations of symptoms that were frequently mentioned together in social media. CONCLUSIONS: Identified outcome-specific risk factors, symptoms, and combinations of symptoms may serve as surrogate indicators to identify patients with COVID-19 and predict their clinical outcomes in order to provide appropriate treatments.