Normalizing Google Scholar data for use in research evaluation.
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ABSTRACT:
SUBMITTER: Mingers J
PROVIDER: S-EPMC5502064 | biostudies-other | 2017
REPOSITORIES: biostudies-other
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Project description:BackgroundGoogle Trends is a novel, freely accessible tool that allows users to interact with Internet search data, which may provide deep insights into population behavior and health-related phenomena. However, there is limited knowledge about its potential uses and limitations. We therefore systematically reviewed health care literature using Google Trends to classify articles by topic and study aim; evaluate the methodology and validation of the tool; and address limitations for its use in research.Methods and findingsPRISMA guidelines were followed. Two independent reviewers systematically identified studies utilizing Google Trends for health care research from MEDLINE and PubMed. Seventy studies met our inclusion criteria. Google Trends publications increased seven-fold from 2009 to 2013. Studies were classified into four topic domains: infectious disease (27% of articles), mental health and substance use (24%), other non-communicable diseases (16%), and general population behavior (33%). By use, 27% of articles utilized Google Trends for casual inference, 39% for description, and 34% for surveillance. Among surveillance studies, 92% were validated against a reference standard data source, and 80% of studies using correlation had a correlation statistic ≥0.70. Overall, 67% of articles provided a rationale for their search input. However, only 7% of articles were reproducible based on complete documentation of search strategy. We present a checklist to facilitate appropriate methodological documentation for future studies. A limitation of the study is the challenge of classifying heterogeneous studies utilizing a novel data source.ConclusionGoogle Trends is being used to study health phenomena in a variety of topic domains in myriad ways. However, poor documentation of methods precludes the reproducibility of the findings. Such documentation would enable other researchers to determine the consistency of results provided by Google Trends for a well-specified query over time. Furthermore, greater transparency can improve its reliability as a research tool.
| S-EPMC4215636 | biostudies-literature
Project description:BACKGROUND:Individuals are increasingly turning to search engines like Google to obtain health information and access resources. Analysis of Google search queries offers a novel approach, which is part of the methodological toolkit for infodemiology or infoveillance researchers, to understanding population health concerns and needs in real time or near-real time. While searches predominantly have been examined with the Google Trends website tool, newer application programming interfaces (APIs) are now available to academics to draw a richer landscape of searches. These APIs allow users to write code in languages like Python to retrieve sample data directly from Google servers. OBJECTIVE:The purpose of this paper is to describe a novel protocol to determine the top queries, volume of queries, and the top sites reached by a population searching on the web for a specific health term. The protocol retrieves Google search data obtained from three Google APIs: Google Trends, Google Health Trends (also referred to as Flu Trends), and Google Custom Search. METHODS:Our protocol consisted of four steps: (1) developing a master list of top search queries for an initial search term using Google Trends, (2) gathering information on relative search volume using Google Health Trends, (3) determining the most popular sites using Google Custom Search, and (4) calculating estimated total search volume. We tested the protocol following key procedures at each step and verified its usefulness by examining search traffic on birth control in 2017 in the United States. Two separate programmers working independently achieved similar results with insignificant variation due to sample variability. RESULTS:We successfully tested the methodology on the initial search term birth control. We identified top search queries for birth control, of which birth control pill was the most popular and obtained the relative and estimated total search volume for the top queries: relative search volume was 0.54 for the pill, corresponding to an estimated 9.3-10.7 million searches. We used the estimates of the proportion of search activity for the top queries to arrive at a generated list of the most popular websites: for the pill, the Planned Parenthood website was the top site. CONCLUSIONS:The proposed methodological framework demonstrates how to retrieve Google query data from multiple Google APIs and provides thorough documentation required to systematically identify search queries and websites, as well as estimate relative and total search volume of queries in real time or near-real time in specific locations and time periods. Although the protocol needs further testing, it allows researchers to replicate the steps and shows promise in advancing our understanding of population-level health concerns. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID):RR1-10.2196/16543.
| S-EPMC7381000 | biostudies-literature
Project description:This study utilise the examination of normal gastro-intestinal tissues to determine a tissue specific signal for use in deriving the intestinal signature of intestinal metaplasias of the oesophagus. Normal oesophageal, colonic and duodenal tissue biopsies were taken after informed consent and RNA was extracted following histological examination of adjacent tissues for normal aperaing mucosa. Three of each tissue type
2013-07-07 | E-GEOD-40220 | biostudies-arrayexpress
Project description:This study utilise the examination of normal gastro-intestinal tissues to determine a tissue specific signal for use in deriving the intestinal signature of intestinal metaplasias of the oesophagus. Normal oesophageal, colonic and duodenal tissue biopsies were taken after informed consent and RNA was extracted following histological examination of adjacent tissues for normal aperaing mucosa.
2013-07-07 | GSE40220 | GEO
Project description:Single-cell transcriptomics is becoming an important component of the molecular biologist's toolkit. A critical step when analyzing data generated using this technology is normalization. However, normalization is typically performed using methods developed for bulk RNA sequencing or even microarray data, and the suitability of these methods for single-cell transcriptomics has not been assessed. We here discuss commonly used normalization approaches and illustrate how these can produce misleading results. Finally, we present alternative approaches and provide recommendations for single-cell RNA sequencing users.
| S-EPMC5549838 | biostudies-literature
Project description:Metabolomics studies of the early-life exposome often use maternal urine specimens to investigate critical developmental windows, including the periconceptional period and early pregnancy. During these windows changes in kidney function can impact urine concentration. This makes accounting for differential urinary dilution across samples challenging. Because there is no consensus on the ideal normalization approach for urinary metabolomics data, this study's objective was to determine the optimal post-analytical normalization approach for untargeted metabolomics analysis from a periconceptional cohort of 45 women. Urine samples consisted of 90 paired pre- and post-implantation samples. After untargeted mass spectrometry-based metabolomics analysis, we systematically compared the performance of three common approaches to adjust for urinary dilution-creatinine adjustment, specific gravity adjustment, and probabilistic quotient normalization (PQN)-using unsupervised principal components analysis, relative standard deviation (RSD) of pooled quality control samples, and orthogonal partial least-squares discriminant analysis (OPLS-DA). Results showed that creatinine adjustment is not a reliable approach to normalize urinary periconceptional metabolomics data. Either specific gravity or PQN are more reliable methods to adjust for urinary concentration, with tighter quality control sample clustering, lower RSD, and better OPLS-DA performance compared to creatinine adjustment. These findings have implications for metabolomics analyses on urine samples taken around the time of conception and in contexts where kidney function may be altered.
| S-EPMC6835889 | biostudies-literature
Project description:BACKGROUND:Data from patients with rare diseases is often produced using different platforms and probe sets because patients are widely distributed in space and time. Aggregating such data requires a method of normalization that makes patient records comparable. RESULTS:This paper proposed DBNorm, implemented as an R package, is an algorithm that normalizes arbitrarily distributed data to a common, comparable form. Specifically, DBNorm merges data distributions by fitting functions to each of them, and using the probability of each element drawn from the fitted distribution to merge it into a global distribution. DBNorm contains state-of-the-art fitting functions including Polynomial, Fourier and Gaussian distributions, and also allows users to define their own fitting functions if required. CONCLUSIONS:The performance of DBNorm is compared with z-score, average difference, quantile normalization and ComBat on a set of datasets, including several that are publically available. The performance of these normalization methods are compared using statistics, visualization, and classification when class labels are known based on a number of self-generated and public microarray datasets. The experimental results show that DBNorm achieves better normalization results than conventional methods. Finally, the approach has the potential to be applicable outside bioinformatics analysis.
| S-EPMC5706403 | biostudies-literature
Project description:BackgroundThe SARS-CoV-2 pandemic has highlighted once more the great need for comprehensive access to, and uncomplicated use of, pre-existing patient data for medical research. Enabling secondary research-use of patient-data is a prerequisite for the efficient and sustainable promotion of translation and personalisation in medicine, and for the advancement of public-health. However, balancing the legitimate interests of scientists in broad and unrestricted data-access and the demand for individual autonomy, privacy and social justice is a great challenge for patient-based medical research.MethodsWe therefore conducted two questionnaire-based surveys among North-German outpatients (n = 650) to determine their attitude towards data-donation for medical research, implemented as an opt-out-process.ResultsWe observed a high level of acceptance (75.0%), the most powerful predictor of a positive attitude towards data-donation was the conviction that every citizen has a duty to contribute to the improvement of medical research (> 80% of participants approving data-donation). Interestingly, patients distinguished sharply between research inside and outside the EU, despite a general awareness that universities and public research institutions cooperate with commercial companies, willingness to allow use of donated data by the latter was very low (7.1% to 29.1%, depending upon location of company). The most popular measures among interviewees to counteract reservations against commercial data-use were regulation by law (61.4%), stipulating in the process that data are not sold or resold (84.6%). A majority requested control of both the use (46.8%) and the protection (41.5%) of the data by independent bodies.ConclusionsIn conclusion, data-donation for medical research, implemented as a combination of legal entitlement and easy-to-exercise-right to opt-out, was found to be widely supported by German patients and therefore warrants further consideration for a transposition into national law.
| S-EPMC8672332 | biostudies-literature
Project description:Online activity-based data can be used to aid infectious disease forecasting. Our aim was to exploit the converging nature of the tuberculosis (TB) and diabetes epidemics to forecast TB case numbers. Thus, we extended TB prediction models based on traditional data with diabetes-related Google searches. We obtained data on the weekly case numbers of TB in Germany from June 8th, 2014, to May 5th, 2019. Internet search data were obtained from a Google Trends (GTD) search for 'diabetes' to the corresponding interval. A seasonal autoregressive moving average (SARIMA) model (0,1,1) (1,0,0) [52] was selected to describe the weekly TB case numbers with and without GTD as an external regressor. We cross-validated the SARIMA models to obtain the root mean squared errors (RMSE). We repeated this procedure with autoregressive feed-forward neural network (NNAR) models using 5-fold cross-validation. To simulate a data-poor surveillance setting, we also tested traditional and GTD-extended models against a hold-out dataset using a decreased 52-week-long period with missing values for training. Cross-validation resulted in an RMSE of 20.83 for the traditional model and 18.56 for the GTD-extended model. Cross-validation of the NNAR models showed a mean RMSE of 19.49 for the traditional model and 18.99 for the GTD-extended model. When we tested the models trained on a decreased dataset with missing values, the GTD-extended models achieved significantly better prediction than the traditional models (p < 0.001). The GTD-extended models outperformed the traditional models in all assessed model evaluation parameters. Using online activity-based data regarding diabetes can improve TB forecasting, but further validation is warranted.
| S-EPMC7480530 | biostudies-literature
Project description:IntroductionIt is often necessary to demonstrate the impact of a research program over time both within and beyond institutions. However, it is difficult to accurately track the publications of research groups over time without significant effort. A simple, scalable, and economical way to track publications from research groups and their metrics would address this challenge.MethodsGoogle Scholar automatically tracks the scholarly output and citation counts of individual researchers. We created Google Scholar profiles to track the scholarly productivity of five research groups: an institutional educational research program, a division of emergency medicine, a department of emergency medicine, a national educational scholarship working group, and an international organization dedicated to online education. We added the publications of each group member to their respective group Google Scholar profile and a junior faculty member monitored the citations that were suggested.ResultsGoogle Scholar tracked a diverse collection of five research groups over 6-36 months. In addition to having different organizational structures and purposes, the groups varied in size, consisting of 8-60 researchers, and prolificacy, with group citation counts between 1006-58,380 and group h‑indexes ranging from 19-101.DiscussionWe anticipate that as this innovation becomes better known it will increasingly be adopted by traditional and non-traditional research groups to easily track their productivity and impact. Additional initiatives will be needed to standardize reporting guidelines within and between institutions.
| S-EPMC6565647 | biostudies-literature