Automatic extraction of quantitative data from ClinicalTrials.gov to conduct meta-analyses

Automatic extraction of quantitative data from ClinicalTrials.gov to conduct meta-analyses. Pradhan, R., Hoaglin, D. C., Cornell, M., Liu, W., Wang, V., & Yu, H. Journal of Clinical Epidemiology, September, 2018.

Paper doi abstract bibtex

Objective Systematic reviews and meta-analyses are labor-intensive and time-consuming. Automated extraction of quantitative data from primary studies can accelerate this process. ClinicalTrials.gov, launched in 2000, is the world’s largest trial repository of results data from clinical trials; it has been used as a source instead of journal articles. We have developed a web application called EXACT that allows users without advanced programming skills to automatically extract data from ClinicalTrials.gov in analysis-ready format. We have also used the automatically extracted data to examine the reproducibility of meta-analyses in three published systematic reviews. Study design We developed a Python-based software application (EXACT, Extracting Accurate efficacy and safety information from ClinicalTrials.gov) that automatically extracts data required for meta-analysis from the ClinicalTrials.gov database in a spreadsheet format. We confirmed the accuracy of the extracted data and then used those data to repeat meta-analyses in three published systematic reviews. To ensure that we used the same statistical methods and outcomes as the published systematic reviews, we repeated the statistics using data manually extracted from the relevant journal articles. For the outcomes whose results we were able to reproduce using those journal article data, we examined the usability of ClinicalTrials.gov data. Results EXACT extracted data at ClincalTrials.gov with 100% accuracy, and it required 60% less time than the usual practice of manually extracting data from journal articles. We found that 87% of the data elements extracted using EXACT matched those extracted manually from the journal articles. We were able to reproduce 24 of 28 outcomes using the journal article data. Of these 24 outcomes, we were able to reproduce 83.3% of the published estimates using data at ClinicalTrials.gov. Conclusion EXACT (http://bio-nlp.org/EXACT) automatically and accurately extracted data elements from ClinicalTrials.gov and thus reduced time in data extraction. The ClinicalTrials.gov data reproduced most meta-analysis results in our study, but this conclusion needs further validation.

@article{pradhan_automatic_2018,
	title = {Automatic extraction of quantitative data from {ClinicalTrials}.gov to conduct meta-analyses},
	volume = {0},
	issn = {0895-4356, 1878-5921},
	url = {https://www.jclinepi.com/article/S0895-4356(17)31306-9/fulltext},
	doi = {10.1016/j.jclinepi.2018.08.023},
	abstract = {Objective
Systematic reviews and meta-analyses are labor-intensive and time-consuming. Automated extraction of quantitative data from primary studies can accelerate this process. ClinicalTrials.gov, launched in 2000, is the world’s largest trial repository of results data from clinical trials; it has been used as a source instead of journal articles. We have developed a web application called EXACT that allows users without advanced programming skills to automatically extract data from ClinicalTrials.gov in analysis-ready format. We have also used the automatically extracted data to examine the reproducibility of meta-analyses in three published systematic reviews.
Study design
We developed a Python-based software application (EXACT, Extracting Accurate efficacy and safety information from ClinicalTrials.gov) that automatically extracts data required for meta-analysis from the ClinicalTrials.gov database in a spreadsheet format. We confirmed the accuracy of the extracted data and then used those data to repeat meta-analyses in three published systematic reviews. To ensure that we used the same statistical methods and outcomes as the published systematic reviews, we repeated the statistics using data manually extracted from the relevant journal articles. For the outcomes whose results we were able to reproduce using those journal article data, we examined the usability of ClinicalTrials.gov data.
Results
EXACT extracted data at ClincalTrials.gov with 100\% accuracy, and it required 60\% less time than the usual practice of manually extracting data from journal articles. We found that 87\% of the data elements extracted using EXACT matched those extracted manually from the journal articles. We were able to reproduce 24 of 28 outcomes using the journal article data. Of these 24 outcomes, we were able to reproduce 83.3\% of the published estimates using data at ClinicalTrials.gov.
Conclusion
EXACT (http://bio-nlp.org/EXACT) automatically and accurately extracted data elements from ClinicalTrials.gov and thus reduced time in data extraction. The ClinicalTrials.gov data reproduced most meta-analysis results in our study, but this conclusion needs further validation.},
	language = {English},
	number = {0},
	urldate = {2018-10-08},
	journal = {Journal of Clinical Epidemiology},
	author = {Pradhan, Richeek and Hoaglin, David C. and Cornell, Matthew and Liu, Weisong and Wang, Victoria and Yu, Hong},
	month = sep,
	year = {2018},
	pmid = {30257185},
	keywords = {Automatic data extraction, ClinicalTrials.gov, Meta-analysis, Reproducibility}
}

Downloads: 0

{"_id":"fXHnmfxRSz5MoZHiT","bibbaseid":"pradhan-hoaglin-cornell-liu-wang-yu-automaticextractionofquantitativedatafromclinicaltrialsgovtoconductmetaanalyses-2018","downloads":0,"creationDate":"2018-10-08T18:00:29.686Z","title":"Automatic extraction of quantitative data from ClinicalTrials.gov to conduct meta-analyses","author_short":["Pradhan, R.","Hoaglin, D. C.","Cornell, M.","Liu, W.","Wang, V.","Yu, H."],"year":2018,"bibtype":"article","biburl":"http://bio-nlp.org/papers/pubs-all.bib","bibdata":{"bibtype":"article","type":"article","title":"Automatic extraction of quantitative data from ClinicalTrials.gov to conduct meta-analyses","volume":"0","issn":"0895-4356, 1878-5921","url":"https://www.jclinepi.com/article/S0895-4356(17)31306-9/fulltext","doi":"10.1016/j.jclinepi.2018.08.023","abstract":"Objective Systematic reviews and meta-analyses are labor-intensive and time-consuming. Automated extraction of quantitative data from primary studies can accelerate this process. ClinicalTrials.gov, launched in 2000, is the world’s largest trial repository of results data from clinical trials; it has been used as a source instead of journal articles. We have developed a web application called EXACT that allows users without advanced programming skills to automatically extract data from ClinicalTrials.gov in analysis-ready format. We have also used the automatically extracted data to examine the reproducibility of meta-analyses in three published systematic reviews. Study design We developed a Python-based software application (EXACT, Extracting Accurate efficacy and safety information from ClinicalTrials.gov) that automatically extracts data required for meta-analysis from the ClinicalTrials.gov database in a spreadsheet format. We confirmed the accuracy of the extracted data and then used those data to repeat meta-analyses in three published systematic reviews. To ensure that we used the same statistical methods and outcomes as the published systematic reviews, we repeated the statistics using data manually extracted from the relevant journal articles. For the outcomes whose results we were able to reproduce using those journal article data, we examined the usability of ClinicalTrials.gov data. Results EXACT extracted data at ClincalTrials.gov with 100% accuracy, and it required 60% less time than the usual practice of manually extracting data from journal articles. We found that 87% of the data elements extracted using EXACT matched those extracted manually from the journal articles. We were able to reproduce 24 of 28 outcomes using the journal article data. Of these 24 outcomes, we were able to reproduce 83.3% of the published estimates using data at ClinicalTrials.gov. Conclusion EXACT (http://bio-nlp.org/EXACT) automatically and accurately extracted data elements from ClinicalTrials.gov and thus reduced time in data extraction. The ClinicalTrials.gov data reproduced most meta-analysis results in our study, but this conclusion needs further validation.","language":"English","number":"0","urldate":"2018-10-08","journal":"Journal of Clinical Epidemiology","author":[{"propositions":[],"lastnames":["Pradhan"],"firstnames":["Richeek"],"suffixes":[]},{"propositions":[],"lastnames":["Hoaglin"],"firstnames":["David","C."],"suffixes":[]},{"propositions":[],"lastnames":["Cornell"],"firstnames":["Matthew"],"suffixes":[]},{"propositions":[],"lastnames":["Liu"],"firstnames":["Weisong"],"suffixes":[]},{"propositions":[],"lastnames":["Wang"],"firstnames":["Victoria"],"suffixes":[]},{"propositions":[],"lastnames":["Yu"],"firstnames":["Hong"],"suffixes":[]}],"month":"September","year":"2018","pmid":"30257185","keywords":"Automatic data extraction, ClinicalTrials.gov, Meta-analysis, Reproducibility","bibtex":"@article{pradhan_automatic_2018,\n\ttitle = {Automatic extraction of quantitative data from {ClinicalTrials}.gov to conduct meta-analyses},\n\tvolume = {0},\n\tissn = {0895-4356, 1878-5921},\n\turl = {https://www.jclinepi.com/article/S0895-4356(17)31306-9/fulltext},\n\tdoi = {10.1016/j.jclinepi.2018.08.023},\n\tabstract = {Objective\nSystematic reviews and meta-analyses are labor-intensive and time-consuming. Automated extraction of quantitative data from primary studies can accelerate this process. ClinicalTrials.gov, launched in 2000, is the world’s largest trial repository of results data from clinical trials; it has been used as a source instead of journal articles. We have developed a web application called EXACT that allows users without advanced programming skills to automatically extract data from ClinicalTrials.gov in analysis-ready format. We have also used the automatically extracted data to examine the reproducibility of meta-analyses in three published systematic reviews.\nStudy design\nWe developed a Python-based software application (EXACT, Extracting Accurate efficacy and safety information from ClinicalTrials.gov) that automatically extracts data required for meta-analysis from the ClinicalTrials.gov database in a spreadsheet format. We confirmed the accuracy of the extracted data and then used those data to repeat meta-analyses in three published systematic reviews. To ensure that we used the same statistical methods and outcomes as the published systematic reviews, we repeated the statistics using data manually extracted from the relevant journal articles. For the outcomes whose results we were able to reproduce using those journal article data, we examined the usability of ClinicalTrials.gov data.\nResults\nEXACT extracted data at ClincalTrials.gov with 100\\% accuracy, and it required 60\\% less time than the usual practice of manually extracting data from journal articles. We found that 87\\% of the data elements extracted using EXACT matched those extracted manually from the journal articles. We were able to reproduce 24 of 28 outcomes using the journal article data. Of these 24 outcomes, we were able to reproduce 83.3\\% of the published estimates using data at ClinicalTrials.gov.\nConclusion\nEXACT (http://bio-nlp.org/EXACT) automatically and accurately extracted data elements from ClinicalTrials.gov and thus reduced time in data extraction. The ClinicalTrials.gov data reproduced most meta-analysis results in our study, but this conclusion needs further validation.},\n\tlanguage = {English},\n\tnumber = {0},\n\turldate = {2018-10-08},\n\tjournal = {Journal of Clinical Epidemiology},\n\tauthor = {Pradhan, Richeek and Hoaglin, David C. and Cornell, Matthew and Liu, Weisong and Wang, Victoria and Yu, Hong},\n\tmonth = sep,\n\tyear = {2018},\n\tpmid = {30257185},\n\tkeywords = {Automatic data extraction, ClinicalTrials.gov, Meta-analysis, Reproducibility}\n}\n\n","author_short":["Pradhan, R.","Hoaglin, D. C.","Cornell, M.","Liu, W.","Wang, V.","Yu, H."],"key":"pradhan_automatic_2018","id":"pradhan_automatic_2018","bibbaseid":"pradhan-hoaglin-cornell-liu-wang-yu-automaticextractionofquantitativedatafromclinicaltrialsgovtoconductmetaanalyses-2018","role":"author","urls":{"Paper":"https://www.jclinepi.com/article/S0895-4356(17)31306-9/fulltext"},"keyword":["Automatic data extraction","ClinicalTrials.gov","Meta-analysis","Reproducibility"],"downloads":0},"search_terms":["automatic","extraction","quantitative","data","clinicaltrials","gov","conduct","meta","analyses","pradhan","hoaglin","cornell","liu","wang","yu"],"keywords":["automatic data extraction","clinicaltrials.gov","meta-analysis","reproducibility"],"authorIDs":[],"dataSources":["NWFE68FH3u4we7mqC"]}