The Glycan Structure Dictionary-a dictionary describing commonly used glycan structure terms.

Recent technological advances in glycobiology have resulted in a large influx of data and the publication of many papers describing discoveries in glycoscience. However, the terms used in describing glycan structural features are not standardized, making it difficult to harmonize data across biomolecular databases, hampering the harvesting of information across studies and hindering text mining and curation efforts. To address this shortcoming, the Glycan Structure Dictionary has been developed as a reference dictionary to provide a standardized list of widely used glycan terms that can help in the curation and mapping of glycan structures described in publications. Currently, the dictionary has 190 glycan structure terms with 297 synonyms linked to 3,332 publications. For a term to be included in the dictionary, it must be present in at least 2 peer-reviewed publications. Synonyms, annotations, and cross-references to GlyTouCan, GlycoMotif, and other relevant databases and resources are also provided when available. The purpose of this effort is to facilitate biocuration, assist in the development of text mining tools, improve the harmonization of search, and browse capabilities in glycoinformatics resources and help to map glycan structures to function and disease. It is also expected that authors will use these terms to describe glycan structures in their manuscripts over time. A mechanism is also provided for researchers to submit terms for potential incorporation. The dictionary is available at https://wiki.glygen.org/Glycan_structure_dictionary.

Investigation of improving the pre-training and fine-tuning of BERT model for biomedical relation extraction.

BACKGROUND: Recently, automatically extracting biomedical relations has been a significant subject in biomedical research due to the rapid growth of biomedical literature. Since the adaptation to the biomedical domain, the transformer-based BERT models have produced leading results on many biomedical natural language processing tasks. In this work, we will explore the approaches to improve the BERT model for relation extraction tasks in both the pre-training and fine-tuning stages of its applications. In the pre-training stage, we add another level of BERT adaptation on sub-domain data to bridge the gap between domain knowledge and task-specific knowledge. Also, we propose methods to incorporate the ignored knowledge in the last layer of BERT to improve its fine-tuning. RESULTS: The experiment results demonstrate that our approaches for pre-training and fine-tuning can improve the BERT model performance. After combining the two proposed techniques, our approach outperforms the original BERT models with averaged F1 score improvement of 2.1% on relation extraction tasks. Moreover, our approach achieves state-of-the-art performance on three relation extraction benchmark datasets. CONCLUSIONS: The extra pre-training step on sub-domain data can help the BERT model generalization on specific tasks, and our proposed fine-tuning mechanism could utilize the knowledge in the last layer of BERT to boost the model performance. Furthermore, the combination of these two approaches further improves the performance of BERT model on the relation extraction tasks.

The phenotypic and haemato-biochemical appraisal of tropical theileriosis in newborn calves.

Tropical theileriosis is one of the major causes of newborn calves mortality. Observation of clinical manifestations is important while making the presumptive/tentative diagnosis of tropical theileriosis in newborn calves. The phenotypic and haemato-biochemical appraisals of tropical theileriosis could be of great help to make a holistic therapeutic plan for diseased newborn calves. Therefore, the present study aimed to evaluate the haemato-biochemical and phenotypic diagnostic markers of tropical theileriosis in newborn calves. A total of 43 newborn calves naturally infected with Theileria annulata and 16 age-matched healthy calves were enrolled. The percentage distribution of clinical markers was generalized lymph nodes enlargement (100%), pyrexia (97.67%), respiratory distress (95.34%), tick infestation (90.69%), anorexia (88.37%), pica (81.39%), pallor mucous membrane (67.44%), hyperlacrimation (58.13%) and exophthalmia (30.22%). Haemograms including TEC, Hb and HCT were found to be significantly (P ≤ 0.001) lowered in diseased calves. Remarkable alterations in the leukogram panels were not observed. Serum glucose, total protein, albumin and globulin concentrations of calves with theileriosis were significantly (P ≤ 0.001) lower than healthy ones, whereas triglycerides and total cholesterol levels of diseased calves were significantly (P ≤ 0.001) higher. Significantly (P ≤ 0.001) elevated activities of serum aspartate aminotransferase (AST), alanine aminotransferase (ALT) and lactate dehydrogenase (LDH) enzymes were observed in diseased calves. An evaluation of clinical phenotypes could be helpful to initiate quick treatment of diseased calves in field conditions and save the lives of sick calves of economically poor farmers. Altered haemato-biochemical panels to be appraised by veterinary clinicians while making a therapeutic plan of tropical theileriosis.

Role of cytokines in the clinical manifestation of exophthalmia in newborn calves with tropical theileriosis.

The present study aimed to evaluate the pathology of the exophthalmia and the host-immune response in naturally Theileria annulata-infected calves. The newborn calves detected positive for theileriosis were grouped into calves with theileriosis and absence of exophthalmia (n = 30), and calves with theileriosis and the presence of exophthalmia (n = 13). Sixteen healthy calves, free from any haemoprotozoal infection, were kept as healthy controls. A significantly (P ≤ .001) higher circulating levels of tumour necrosis factor-α (TNF-α) and interleukin-10 (IL-10) were estimated in diseased calves with and without exophthalmia as compared to healthy controls. Contrarily, significantly (P ≤ .01) lower interferon-γ (IFN-γ) level was estimated in diseased calves. The diseased calves with exophthalmia revealed significantly higher levels of TNF-α (P ≤ .001) and IL-10 (P ≤ .006) as compared to the diseased calves without exophthalmia. The diseased calves were not found to have an elevated intraocular pressure; rather they had significantly (P ≤ .001) lower intraocular pressure compared to the healthy controls. An elevated systemic TNF-α level might be attributed to the exophthalmia in calves with tropical theileriosis. The elevated circulatory IL-10 and reduced IFN-γ levels could be one of the strategies of Theileria annulata to escape the host immunity.

Synthesis and biological evaluation of imidazoline derivatives as potential CNS and CVS agents.

A series of substituted imidazoline derivatives were synthesized and characterized. Compounds were tested in-vivo for their antihypertensive, analgesic, antiaggressive, depressant, antidepressant, and ALD50 activities. The compounds 3a, 3c, 4c, 5a, and 6c showed cardiovascular as well as central nervous system activities and are potential candidate as drug among all fifteen compounds tested. All these compounds have shown better activity for antihypertensive, analgesic, antiaggressive, and depressant-antidepressant, properties than reference compounds clonidine, morphine, diazepam, and imipramine respectively. Most of the compounds have shown ALD50 > 500 mg/kg with maximum in 4a and 5a (>1000 mg/kg).

Endophytes enhance the production of root alkaloids ajmalicine and serpentine by modulating the terpenoid indole alkaloid pathway in Catharanthus roseus roots.

AIM: The aim of this study was to identify and characterize promising endophytes capable of enhancing the content of root alkaloids ajmalicine and serpentine in low alkaloid yielding genotype of Catharanthus roseus cultivar Prabal and the possible mechanisms involved. METHOD AND RESULT: Of the four strains isolated from alkaloid-rich genotype of C. roseus cultivar Dhawal, endophytic strains CATDLF5 (Curvularia sp.) and CATDLF6 (Choanephora infundibulifera) enhanced serpentine content by 211·7-337·6%, while CATDRF2 (Aspergillus japonicus) and CATDS5 (Pseudomonas sp.) increased the content of ajmalicine by 123·4-203·8% in cultivar Prabal. Upregulated expression of key genes, geraniol 10-hydroxylase, tryptophan decarboxylase and strictosidine synthase involved in terpenoid indole alkaloid (TIA) biosynthetic pathway was observed in endophyte inoculated plants. Upregulated Octadecanoid-derivative Responsive Catharanthus AP2/ERF domain transcription activators like ORCA3 while, and downregulation of transcriptional repressor, ZCTs (Cys2/His2-type zinc finger protein family) enhanced the expression of genes for secondary metabolite production in endophyte-inoculated plants. CONCLUSION: The present work concluded that the selected endophytes of C. roseus can enhance the ajmalicine and serpentine contents by modulating the expression of structural and regulatory genes of TIA biosynthetic pathway in root. SIGNIFICANCE AND IMPACT OF THE STUDY: Endophytes can play an important role to enhance in planta content of pharmaceutically important alkaloids in C. roseus and can therefore be useful in reducing the cost of production of important alkaloids.

iPTMnet: an integrated resource for protein post-translational modification network discovery.

Protein post-translational modifications (PTMs) play a pivotal role in numerous biological processes by modulating regulation of protein function. We have developed iPTMnet (http://proteininformationresource.org/iPTMnet) for PTM knowledge discovery, employing an integrative bioinformatics approach-combining text mining, data mining, and ontological representation to capture rich PTM information, including PTM enzyme-substrate-site relationships, PTM-specific protein-protein interactions (PPIs) and PTM conservation across species. iPTMnet encompasses data from (i) our PTM-focused text mining tools, RLIMS-P and eFIP, which extract phosphorylation information from full-scale mining of PubMed abstracts and full-length articles; (ii) a set of curated databases with experimentally observed PTMs; and iii) Protein Ontology that organizes proteins and PTM proteoforms, enabling their representation, annotation and comparison within and across species. Presently covering eight major PTM types (phosphorylation, ubiquitination, acetylation, methylation, glycosylation, S-nitrosylation, sumoylation and myristoylation), iPTMnet knowledgebase contains more than 654 500 unique PTM sites in over 62 100 proteins, along with more than 1200 PTM enzymes and over 24 300 PTM enzyme-substrate-site relations. The website supports online search, browsing, retrieval and visual analysis for scientific queries. Several examples, including functional interpretation of phosphoproteomic data, demonstrate iPTMnet as a gateway for visual exploration and systematic analysis of PTM networks and conservation, thereby enabling PTM discovery and hypothesis generation.

Alterations in circulating concentrations of IL-17, IL-31 and total IgE in dogs with atopic dermatitis.

BACKGROUND: The pathogenesis of canine atopic dermatitis (AD) is complex. Dysregulation of the cutaneous immune system is considered an important regulator of the allergic response. Exploration of association of interleukin-17 (IL-17), IL-31, IgE and leukogram attributes with canine AD could provide novel insights into its immunopathology. HYPOTHESIS/OBJECTIVES: To investigate possible associations of IL-17, IL-3, IgE and leukogram attributes of canine AD. ANIMALS: 17 dogs diagnosed with AD and six healthy dogs. METHODS AND MATERIALS: Circulating concentrations of IL-17, IL-31 and total IgE from sera samples were determined using commercial canine-specific quantitative immunoassay kits. Complete blood cell counts were analysed by an automated haematology analyser. Statistical differences between the two groups were determined using an unpaired t-test. The degree of relationship between the IL-17, IL-31, IgE, total leukocyte count (TLC) values and clinical signs scores (Canine Atopic Dermatitis Lesion Index and pruritus Visual Analog Scale pVAS) was determined by Pearson's r correlation statistic. RESULTS: Dogs with AD had significantly (P < 0.0001) higher circulating concentrations of IL-17, IL-31 and total IgE compared with healthy dogs. Dogs with AD also had significantly higher TLC (P < 0.0002), absolute neutrophils (P < 0.0001) and absolute eosinophils (P < 0.0001) counts, and percentage of neutrophils (P < 0.03) and eosinophils (P < 0.0001) compared with healthy controls. A significant positive correlation (r2  = 0.396; P < 0.007) between the pVAS and IL-31 was observed in dogs with AD. CONCLUSIONS AND CLINICAL IMPORTANCE: Marked elevation in circulating IL-17, IL-31 and total IgE along with the abnormalities in leukogram may be associated with canine AD and could be possible targets in the therapeutic management of canine AD.

Superglue slide impression (SSI) method: a novel diagnostic application for canine demodicosis.

The conventional gold standard diagnostic method for canine demodicosis, the deep skin scrapings (DSS), is traumatic to the animal and appears aggressive in the eyes of the owner. A less invasive, sensitive, easy-to-perform and field-oriented diagnostic method for the rapid diagnosis of canine demodicosis is warranted. The present study aimed to develop a rapid less invasive diagnostic method using superglue (cyanoacrylate adhesive) slide impression (SSI). Ninety-seven client-owned dogs presented with clinical symptoms and signs suggestive of demodicosis were examined using SSI for detection of Demodex mites. A clean microscope slide was taken and a drop of superglue was placed on the slide. Immediately, the superglue-bearing slide surface was applied to the previously squeezed selected skin lesion with gentle pressure for 30 s. The slide was removed from the skin lesion and a drop of immersion oil was placed over the SSI. Another clean cover slide was applied and examined under the microscope at low-power magnification (× 10 lens). Of the 97 dogs, 90 dogs (92.8%) were detected positive for demodectic mites using the SSI method, whereas 86 (88.7%) dogs were found positive using the DSS technique. The SSI method was found to be equally sensitive to the DSS method. In summary, the SSI method is a new quick, sensitive, easy-to-perform, owner- and animal-friendly, less traumatic and field-oriented diagnostic application for demodicosis in dogs. It can be used for harvesting the live demodectic mites and monitoring miticidal therapies.

Automatic gene annotation using GO terms from cellular component domain.

BACKGROUND: The Gene Ontology (GO) is a resource that supplies information about gene product function using ontologies to represent biological knowledge. These ontologies cover three domains: Cellular Component (CC), Molecular Function (MF), and Biological Process (BP). GO annotation is a process which assigns gene functional information using GO terms to relevant genes in the literature. It is a common task among the Model Organism Database (MOD) groups. Manual GO annotation relies on human curators assigning gene functional information using GO terms by reading the biomedical literature. This process is very time-consuming and labor-intensive. As a result, many MODs can afford to curate only a fraction of relevant articles. METHODS: GO terms from the CC domain can be essentially divided into two sub-hierarchies: subcellular location terms, and protein complex terms. We cast the task of gene annotation using GO terms from the CC domain as relation extraction between gene and other entities: (1) extract cases where a protein is found to be in a subcellular location, and (2) extract cases where a protein is a subunit of a protein complex. For each relation extraction task, we use an approach based on triggers and syntactic dependencies to extract the desired relations among entities. RESULTS: We tested our approach on the BC4GO test set, a publicly available corpus for GO annotation. Our approach obtains a F1-score of 71%, a precision of 91% and a recall of 58% for predicting GO terms from CC Domain for given genes. CONCLUSIONS: We have described a novel approach of treating gene annotation with GO terms from CC domain as two relation extraction subtasks. Evaluation results show that our approach achieves a F1-score of 71% for predicting GO terms for given genes. Thereby our approach can be used to accelerate the process of GO annotation for the bio-annotators.

WebGIVI: a web-based gene enrichment analysis and visualization tool.

BACKGROUND: A major challenge of high throughput transcriptome studies is presenting the data to researchers in an interpretable format. In many cases, the outputs of such studies are gene lists which are then examined for enriched biological concepts. One approach to help the researcher interpret large gene datasets is to associate genes and informative terms (iTerm) that are obtained from the biomedical literature using the eGIFT text-mining system. However, examining large lists of iTerm and gene pairs is a daunting task. RESULTS: We have developed WebGIVI, an interactive web-based visualization tool ( http://raven.anr.udel.edu/webgivi/ ) to explore gene:iTerm pairs. WebGIVI was built via Cytoscape and Data Driven Document JavaScript libraries and can be used to relate genes to iTerms and then visualize gene and iTerm pairs. WebGIVI can accept a gene list that is used to retrieve the gene symbols and corresponding iTerm list. This list can be submitted to visualize the gene iTerm pairs using two distinct methods: a Concept Map or a Cytoscape Network Map. In addition, WebGIVI also supports uploading and visualization of any two-column tab separated data. CONCLUSIONS: WebGIVI provides an interactive and integrated network graph of gene and iTerms that allows filtering, sorting, and grouping, which can aid biologists in developing hypothesis based on the input gene lists. In addition, WebGIVI can visualize hundreds of nodes and generate a high-resolution image that is important for most of research publications. The source code can be freely downloaded at https://github.com/sunliang3361/WebGIVI . The WebGIVI tutorial is available at http://raven.anr.udel.edu/webgivi/tutorial.php .

Immunomodulatory basis of antioxidant therapy and its future prospects: an appraisal.

Antioxidants are agents which can modulate oxidant-antioxidant profile of body system by neutralizing pro-oxidant molecules. The current scientific knowledge on mechanisms of antioxidant activity of biomolecules was critically reviewed with a special emphasis on immunomodulation. The immuno-oxidative wreckage of animals in various disease conditions and the role of biomodulators in curbing the oxidative stress through immune pathways were analyzed. The critical role of immunomodulatory mechanisms in controlling oxidative damage was identified. Selection of antioxidant therapy considering the immunopharmacology of the drug as well as immunological basis of disease may reduce treatment failure and adverse health effects. Hence, it is suggested that future studies on antioxidants may focus on the immuno-oxidative pathobiology to better understand its clinical effects and effective disease management.

miRTex: A Text Mining System for miRNA-Gene Relation Extraction.

MicroRNAs (miRNAs) regulate a wide range of cellular and developmental processes through gene expression suppression or mRNA degradation. Experimentally validated miRNA gene targets are often reported in the literature. In this paper, we describe miRTex, a text mining system that extracts miRNA-target relations, as well as miRNA-gene and gene-miRNA regulation relations. The system achieves good precision and recall when evaluated on a literature corpus of 150 abstracts with F-scores close to 0.90 on the three different types of relations. We conducted full-scale text mining using miRTex to process all the Medline abstracts and all the full-length articles in the PubMed Central Open Access Subset. The results for all the Medline abstracts are stored in a database for interactive query and file download via the website at http://proteininformationresource.org/mirtex. Using miRTex, we identified genes potentially regulated by miRNAs in Triple Negative Breast Cancer, as well as miRNA-gene relations that, in conjunction with kinase-substrate relations, regulate the response to abiotic stress in Arabidopsis thaliana. These two use cases demonstrate the usefulness of miRTex text mining in the analysis of miRNA-regulated biological processes.

Detection of Peste Des Petits Ruminants Virus (PPRV) Genome from Nasal Swabs of Dogs.

Peste des petits ruminants virus (PPRV) one of the most important viruses of small ruminants has a restricted host range. We report here the presence of PPRV virus in the nasal swabs of 3 out of 12 dogs in a routine microarray screening. The presence of PPRV sequence was further confirmed by PCR and sequencing. The sequence analysis revealed that the PPRV virus has close similarities with the viruses present in Indian subcontinent but was not identical to the vaccine virus used in India. Results suggest possible crossing of species barrier but requires further serological evidences.

A generalizable NLP framework for fast development of pattern-based biomedical relation extraction systems.

BACKGROUND: Text mining is increasingly used in the biomedical domain because of its ability to automatically gather information from large amount of scientific articles. One important task in biomedical text mining is relation extraction, which aims to identify designated relations among biological entities reported in literature. A relation extraction system achieving high performance is expensive to develop because of the substantial time and effort required for its design and implementation. Here, we report a novel framework to facilitate the development of a pattern-based biomedical relation extraction system. It has several unique design features: (1) leveraging syntactic variations possible in a language and automatically generating extraction patterns in a systematic manner, (2) applying sentence simplification to improve the coverage of extraction patterns, and (3) identifying referential relations between a syntactic argument of a predicate and the actual target expected in the relation extraction task. RESULTS: A relation extraction system derived using the proposed framework achieved overall F-scores of 72.66% for the Simple events and 55.57% for the Binding events on the BioNLP-ST 2011 GE test set, comparing favorably with the top performing systems that participated in the BioNLP-ST 2011 GE task. We obtained similar results on the BioNLP-ST 2013 GE test set (80.07% and 60.58%, respectively). We conducted additional experiments on the training and development sets to provide a more detailed analysis of the system and its individual modules. This analysis indicates that without increasing the number of patterns, simplification and referential relation linking play a key role in the effective extraction of biomedical relations. CONCLUSIONS: In this paper, we present a novel framework for fast development of relation extraction systems. The framework requires only a list of triggers as input, and does not need information from an annotated corpus. Thus, we reduce the involvement of domain experts, who would otherwise have to provide manual annotations and help with the design of hand crafted patterns. We demonstrate how our framework is used to develop a system which achieves state-of-the-art performance on a public benchmark corpus.

Amelioration of altered oxidant/antioxidant balance of Indian water buffaloes with subclinical mastitis by vitamins A, D3, E, and H supplementation.

The effect of vitamins A, D3, E, and H supplementation on oxidative stress indices in Indian water buffaloes suffering from subclinical mastitis was investigated. Changes in the total oxidant capacity (TOC), total antioxidant capacity (TAC), nitric oxide (NO), and activities of glutathione peroxidase (GSH-Px), catalase (CAT), and superoxide dismutase (SOD) in milk were evaluated before and after the supplementation of vitamins A, D3, E, and H. The buffaloes suffering from subclinical mastitis revealed remarkable alterations in the milk oxidants/antioxidants balance shifted towards oxidative status. The buffaloes with subclinical mastitis revealed significantly (P ≤ 0.01) higher TOC, NO contents, and CAT activity, while TAC content and GSH-Px activity were significantly (P ≤ 0.01) lower in comparison with the healthy controls. However, SOD activity did not show any significant change. Supplementation of vitamins A, D3, E, and H to these animals revealed significant (P ≤ 0.01) reduction in TOC, NO, and CAT, while a significant (P ≤ 0.01) increase in TAC and GSH-Px activity was also evident. From the present study, it may be concluded that supplementation of these vitamins can help ameliorate the altered milk oxidants/antioxidants balance towards normalcy and, thus, ensue recovery from subclinical mastitis in the Indian water buffaloes.

Text mining of CHO bioprocess bibliome: Topic modeling and document classification.

Chinese hamster ovary (CHO) cells are widely used for mass production of therapeutic proteins in the pharmaceutical industry. With the growing need in optimizing the performance of producer CHO cell lines, research on CHO cell line development and bioprocess continues to increase in recent decades. Bibliographic mapping and classification of relevant research studies will be essential for identifying research gaps and trends in literature. To qualitatively and quantitatively understand the CHO literature, we have conducted topic modeling using a CHO bioprocess bibliome manually compiled in 2016, and compared the topics uncovered by the Latent Dirichlet Allocation (LDA) models with the human labels of the CHO bibliome. The results show a significant overlap between the manually selected categories and computationally generated topics, and reveal the machine-generated topic-specific characteristics. To identify relevant CHO bioprocessing papers from new scientific literature, we have developed supervized models using Logistic Regression to identify specific article topics and evaluated the results using three CHO bibliome datasets, Bioprocessing set, Glycosylation set, and Phenotype set. The use of top terms as features supports the explainability of document classification results to yield insights on new CHO bioprocessing papers.

Therapeutic effects of oral fluralaner in pet rabbits with severe sarcoptic mange (Sarcoptes scabiei).

Sarcoptic mange is one of the most severe, highly contagious, and fatal ectoparasitic infestations of rabbits. Fluralaner, an isoxazoline class of oral ectoparasiticide, is considered as a very potent acaricide. The present study aimed to evaluate the therapeutic efficacy of oral fluralaner in pet rabbits with severe spontaneous Sarcoptes scabiei infestation. A total of eight un-neutered pet rabbits, tested positive for S. scabiei by microscopy of skin scrapings, were enrolled. Seven rabbits had severe clinical infestation (score 5), while remaining one rabbit had moderate disease clinical signs (score <3). A single oral dose equivalent to 25 mg/kg of fluralaner was administered to each rabbit. On day 14 post-therapy, marked improvements in the skin lesions were observed; severely infested rabbits had a clinical score of 3, while the moderately infested rabbit had a score of 1. However, none of the rabbits tested negative for S. scabiei. On day 30 post-therapy, complete clinical recovery was recorded in all rabbits (Score 0), but, a complete parasitological clearance was not recorded except to the moderately infested rabbit. All rabbits were tested negative for S. scabiei on day 45 post-therapy. Therefore, a single oral dose of fluralaner at a 25 mg/kg was found to be effective in the treatment of severe sarcoptic mange in pet rabbits and no additional topical or systemic medications were needed. Further studies in a larger number of individuals with a bigger spectrum of disease severities (i.e. more moderate/mild) are needed to comprehensively document the safety and efficacy of this drug in mangy rabbits.

Substituted imidazole derivatives as novel cardiovascular agents.

A series of novel substituted imidazole derivatives were synthesized and have been screened in vivo for their hypotensive and acute toxicity activities. Out of seventeen compounds eight compounds (2b, 2c, 3b, 3c, 3f, 4a, 4b and 4c) have shown good hypotensive and bradycardiac responses. Compounds 3b, 3c, 3f and 4c have shown better activity than reference drug clonidine. All the compounds have shown ALD50>1000 mg/kg with maximum in 2e and 4c (>1200 mg/kg).

emiRIT: a text-mining-based resource for microRNA information.

microRNAs (miRNAs) are essential gene regulators, and their dysregulation often leads to diseases. Easy access to miRNA information is crucial for interpreting generated experimental data, connecting facts across publications and developing new hypotheses built on previous knowledge. Here, we present extracting miRNA Information from Text (emiRIT), a text-miningbased resource, which presents miRNA information mined from the literature through a user-friendly interface. We collected 149 ,233 miRNA -PubMed ID pairs from Medline between January 1997 and May 2020. emiRIT currently contains 'miRNA -gene regulation' (69 ,152 relations), 'miRNA disease (cancer)' (12 ,300 relations), 'miRNA -biological process and pathways' (23, 390 relations) and circulatory 'miRNAs in extracellular locations' (3782 relations). Biological entities and their relation to miRNAs were extracted from Medline abstracts using publicly available and in-house developed text-mining tools, and the entities were normalized to facilitate querying and integration. We built a database and an interface to store and access the integrated data, respectively. We provide an up-to-date and user-friendly resource to facilitate access to comprehensive miRNA information from the literature on a large scale, enabling users to navigate through different roles of miRNA and examine them in a context specific to their information needs. To assess our resource's information coverage, we have conducted two case studies focusing on the target and differential expression information of miRNAs in the context of cancer and a third case study to assess the usage of emiRIT in the curation of miRNA information. Database URL: https://research.bioinformatics.udel.edu/emirit/.