OrganoidDB: a comprehensive organoid database for the multi-perspective exploration of bulk and single-cell transcriptomic profiles of organoids.

Organoids, three-dimensional in vitro tissue cultures derived from pluripotent (embryonic or induced) or adult stem cells, are promising models for the study of human processes and structures, disease onset and preclinical drug development. An increasing amount of omics data has been generated for organoid studies. Here, we introduce OrganoidDB (http://www.inbirg.com/organoid_db/), a comprehensive resource for the multi-perspective exploration of the transcriptomes of organoids. The current release of OrganoidDB includes curated bulk and single-cell transcriptome profiles of 16 218 organoid samples from both human and mouse. Other types of samples, such as primary tissue and cell line samples, are also integrated to enable comparisons with organoids. OrganoidDB enables queries of gene expression under different modes, e.g. across different organoid types, between different organoids from different sources or protocols, between organoids and other sample types, across different development stages, and via correlation analysis. Datasets and organoid samples can also be browsed for detailed information, including organoid information, differentially expressed genes, enriched pathways and single-cell clustering. OrganoidDB will facilitate a better understanding of organoids and help improve organoid culture protocols to yield organoids that are highly similar to living organs in terms of composition, architecture and function.

PertOrg 1.0: a comprehensive resource of multilevel alterations induced in model organisms by in vivo genetic perturbation.

Genetically modified organisms (GMOs) can be generated to model human genetic disease or plant disease resistance, and they have contributed to the exploration and understanding of gene function, physiology, disease onset and drug target discovery. Here, PertOrg (http://www.inbirg.com/pertorg/) was introduced to provide multilevel alterations in GMOs. Raw data of 58 707 transcriptome profiles and associated information, such as phenotypic alterations, were collected and curated from studies involving in vivo genetic perturbation (e.g. knockdown, knockout and overexpression) in eight model organisms, including mouse, rat and zebrafish. The transcriptome profiles from before and after perturbation were organized into 10 116 comparison datasets, including 122 single-cell RNA-seq datasets. The raw data were checked and analysed using widely accepted and standardized pipelines to identify differentially expressed genes (DEGs) in perturbed organisms. As a result, 8 644 148 DEGs were identified and deposited as signatures of gene perturbations. Downstream functional enrichment analysis, cell type analysis and phenotypic alterations were also provided when available. Multiple search methods and analytical tools were created and implemented. Furthermore, case studies were presented to demonstrate how users can utilize the database. PertOrg 1.0 will be a valuable resource aiding in the exploration of gene functions, biological processes and disease models.

DDPD 1.0: a manually curated and standardized database of digital properties of approved drugs for drug-likeness evaluation and drug development.

Drug-likeness is a vital consideration when selecting compounds in the early stage of drug discovery. A series of drug-like properties are needed to predict the drug-likeness of a given compound and provide useful guidelines to increase the likelihood of converting lead compounds into drugs. Experimental physicochemical properties, pharmacokinetic/toxicokinetic properties and maximum dosages of approved small-molecule drugs from multiple text-based unstructured data resources have been manually assembled, curated, further digitized and processed into structured data, which are deposited in the Database of Digital Properties of approved Drugs (DDPD). DDPD 1.0 contains 30 212 drug property entries, including 2250 approved drugs and 32 properties, in a standardized value/unit format. Moreover, two analysis tools are provided to examine the drug-likeness features of given molecules based on the collected property data of approved drugs. Additionally, three case studies are presented to demonstrate how users can utilize the database. We believe that this database will be a valuable resource for the drug discovery and development field. Database URL:  http://www.inbirg.com/ddpd.

Geographic Differences in Cannabis Conversations on Twitter: Infodemiology Study.

BACKGROUND: Infodemiology is an emerging field of research that utilizes user-generated health-related content, such as that found in social media, to help improve public health. Twitter has become an important venue for studying emerging patterns in health issues such as substance use because it can reflect trends in real-time and display messages generated directly by users, giving a uniquely personal voice to analyses. Over the past year, several states in the United States have passed legislation to legalize adult recreational use of cannabis and the federal government in Canada has done the same. There are few studies that examine the sentiment and content of tweets about cannabis since the recent legislative changes regarding cannabis have occurred in North America. OBJECTIVE: To examine differences in the sentiment and content of cannabis-related tweets by state cannabis laws, and to examine differences in sentiment between the United States and Canada between 2017 and 2019. METHODS: In total, 1,200,127 cannabis-related tweets were collected from January 1, 2017, to June 17, 2019, using the Twitter application programming interface. Tweets then were grouped geographically based on cannabis legal status (legal for adult recreational use, legal for medical use, and no legal use) in the locations from which the tweets came. Sentiment scoring for the tweets was done with VADER (Valence Aware Dictionary and sEntiment Reasoner), and differences in sentiment for states with different cannabis laws were tested using Tukey adjusted two-sided pairwise comparisons. Topic analysis to determine the content of tweets was done using latent Dirichlet allocation in Python, using a Java implementation, LdaMallet, with Gensim wrapper. RESULTS: Significant differences were seen in tweet sentiment between US states with different cannabis laws (P=.001 for negative sentiment tweets in fully illegal compared to legal for adult recreational use states), as well as between the United States and Canada (P=.003 for positive sentiment and P=.001 for negative sentiment). In both cases, restrictive state policy environments (eg, those where cannabis use is fully illegal, or legal for medical use only) were associated with more negative tweet sentiment than less restrictive policy environments (eg, where cannabis is legal for adult recreational use). Six key topics were found in recent US tweet contents: fun and recreation (keywords, eg, love, life, high); daily life (today, start, live); transactions (buy, sell, money); places of use (room, car, house); medical use and cannabis industry (business, industry, company); and legalization (legalize, police, tax). The keywords representing content of tweets also differed between the United States and Canada. CONCLUSIONS: Knowledge about how cannabis is being discussed online, and geographic differences that exist in these conversations may help to inform public health planning and prevention efforts. Public health education about how to use cannabis in ways that promote safety and minimize harms may be especially important in places where cannabis is legal for adult recreational and medical use.