scholarly journals Corrigendum to: the SNPcurator: literature mining of enriched SNP-disease associations

Database ◽  
2021 ◽  
Vol 2021 (2021) ◽  
Author(s):  
Noha S Tawfik ◽  
Marco R Spruit
Keyword(s):  
Literature Mining ◽  
Disease Associations

scholarly journals Literature Evidence in Open Targets – a target validation platform

2017 ◽  
Author(s):  
Şenay Kafkas ◽  
Ian Dunham ◽  
Johanna McEntyre
Keyword(s):  
Drug Target ◽  
Target Identification ◽  
Relevant Literature ◽  
Literature Mining ◽  
Target Validation ◽  
Link Type ◽  
Drug Target Identification ◽  
Disease Associations ◽  
Target Disease ◽  
Literature Evidence

AbstractBackgroundWe present the Europe PMC literature component of Open Targets – a target validation platform that integrates various evidence to aid drug target identification and validation. The component identifies target-disease associations in documents and ranks the documents based on their confidence from the Europe PMC literature database, by using rules utilising expert-provided heuristic information and serves the platform regularly with the up-to-date data since December, 2015.ResultsCurrently, there are a total number of 1168365 distinct target-disease associations text mined from >26 million PubMed abstracts and >1.2 million Open Access full text articles. Our comparative analyses on the current available evidence data in the platform revealed that 850179 of these associations are exclusively identified by literature mining.ConclusionThis component helps the platform’s users by providing the most relevant literature hits for a given target and disease. The text mining evidence along with the other types of evidence can be explored visually through https://www.targetvalidation.org and all the evidence data is available for download in json format from https://www.targetvalidation.org/downloads/data.

scholarly journals The SNPcurator: literature mining of enriched SNP-disease associations

Database ◽  
2018 ◽  
Vol 2018 ◽  
Author(s):  
Noha S Tawfik ◽  
Marco R Spruit
Keyword(s):  
Literature Mining ◽  
Disease Associations

scholarly journals Predicting LncRNA–Disease Association by a Random Walk With Restart on Multiplex and Heterogeneous Networks

2021 ◽  
Vol 12 ◽  
Author(s):  
Yuhua Yao ◽  
Binbin Ji ◽  
Yaping Lv ◽  
Ling Li ◽  
Ju Xiang ◽  
...  
Keyword(s):  
Random Walk ◽  
Heterogeneous Networks ◽  
Heterogeneous Network ◽  
Computational Models ◽  
Literature Mining ◽  
Random Walk With Restart ◽  
Disease Similarity ◽  
Disease Associations ◽  
Similarity Networks ◽  
Similarity Scores

Studies have found that long non-coding RNAs (lncRNAs) play important roles in many human biological processes, and it is critical to explore potential lncRNA–disease associations, especially cancer-associated lncRNAs. However, traditional biological experiments are costly and time-consuming, so it is of great significance to develop effective computational models. We developed a random walk algorithm with restart on multiplex and heterogeneous networks of lncRNAs and diseases to predict lncRNA–disease associations (MHRWRLDA). First, multiple disease similarity networks are constructed by using different approaches to calculate similarity scores between diseases, and multiple lncRNA similarity networks are also constructed by using different approaches to calculate similarity scores between lncRNAs. Then, a multiplex and heterogeneous network was constructed by integrating multiple disease similarity networks and multiple lncRNA similarity networks with the lncRNA–disease associations, and a random walk with restart on the multiplex and heterogeneous network was performed to predict lncRNA–disease associations. The results of Leave-One-Out cross-validation (LOOCV) showed that the value of Area under the curve (AUC) was 0.68736, which was improved compared with the classical algorithm in recent years. Finally, we confirmed a few novel predicted lncRNAs associated with specific diseases like colon cancer by literature mining. In summary, MHRWRLDA contributes to predict lncRNA–disease associations.

Pharmacokinetic Drug-drug Interaction of Antibiotics Used in Sepsis Care in China

2020 ◽  
Vol 21 ◽  
Author(s):  
Xuan Yu ◽  
Zixuan Chu ◽  
Jian Li ◽  
Rongrong He ◽  
Yaya Wang ◽  
...  
Keyword(s):  
Drug Interaction ◽  
Drug Interactions ◽  
Penicillin G ◽  
Literature Mining ◽  
Human Pharmacokinetics ◽  
P450 Enzyme ◽  
Drug Drug Interaction ◽  
Pharmacokinetic Drug ◽  
Sepsis Care

Background: Many antibiotics have a high potential for having an interaction with drugs, as perpetrator and/or victim, in critically ill patients, and particularly in sepsis patients. Methods: The aim of this review is to summarize the pharmacokinetic drug-drug interaction (DDI) of 45 antibiotics commonly used in sepsis care in China. Literature mining was conducted to obtain human pharmacokinetics/dispositions of the antibiotics, their interactions with drug metabolizing enzymes or transporters, and their associated clinical drug interactions. Potential DDI is indicated by a DDI index > 0.1 for inhibition or a treated-cell/untreated-cell ratio of enzyme activity being > 2 for induction. Results: The literature-mined information on human pharmacokinetics of the identified antibiotics and their potential drug interactions is summarized. Conclusion: Antibiotic-perpetrated drug interactions, involving P450 enzyme inhibition, have been reported for four lipophilic antibacterials (ciprofloxacin, erythromycin, trimethoprim, and trimethoprim-sulfamethoxazole) and three lipophilic antifungals (fluconazole, itraconazole, and voriconazole). In addition, seven hydrophilic antibacterials (ceftriaxone, cefamandole, piperacillin, penicillin G, amikacin, metronidazole, and linezolid) inhibit drug transporters in vitro. Despite no reported clinical PK drug interactions with the transporters, caution is advised in the use of these antibacterials. Eight hydrophilic antibacterials (all β-lactams; meropenem, cefotaxime, cefazolin, piperacillin, ticarcillin, penicillin G, ampicillin, and flucloxacillin), are potential victims of drug interactions due to transporter inhibition. Rifampin is reported to perpetrate drug interactions by inducing CYP3A or inhibiting OATP1B; it is also reported to be a victim of drug interactions, due to the dual inhibition of CYP3A4 and OATP1B by indinavir. In addition, three antifungals (caspofungin, itraconazole, and voriconazole) are reported to be victims of drug interactions because of P450 enzyme induction. Reports for other antibiotics acting as victims in drug interactions are scarce.

EHAI: Enhanced Human Microbe-Disease Association Identification

2020 ◽  
Vol 21 (11) ◽  
pp. 1078-1084
Author(s):  
Ruizhi Fan ◽  
Chenhua Dong ◽  
Hu Song ◽  
Yixin Xu ◽  
Linsen Shi ◽  
...  
Keyword(s):  
Microbial Community ◽  
Human Health ◽  
Complex Diseases ◽  
Disease Association ◽  
Computational Results ◽  
Computational Approaches ◽  
Disease Diagnostics ◽  
Disease Associations ◽  
Association Discovery ◽  
Biological Tool

: Recently, an increasing number of biological and clinical reports have demonstrated that imbalance of microbial community has the ability to play important roles among several complex diseases concerning human health. Having a good knowledge of discovering potential of microbe-disease relationships, which provides the ability to having a better understanding of some issues, including disease pathology, further boosts disease diagnostics and prognostics, has been taken into account. Nevertheless, a few computational approaches can meet the need of huge scale of microbe-disease association discovery. In this work, we proposed the EHAI model, which is Enhanced Human microbe- disease Association Identification. EHAI employed the microbe-disease associations, and then Gaussian interaction profile kernel similarity has been utilized to enhance the basic microbe-disease association. Actually, some known microbe-disease associations and a large amount of associations are still unavailable among the datasets. The ‘super-microbe’ and ‘super-disease’ were employed to enhance the model. Computational results demonstrated that such super-classes have the ability to be helpful to the performance of EHAI. Therefore, it is anticipated that EHAI can be treated as an important biological tool in this field.

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