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README.md

2019-02-clinical-trials

R-Script & data

The preprocessing and analysis of the data was conducted in the R project for statistical computing. The RMarkdown script used to generate this document and all the resulting data can be downloaded under this link. Through executing main.Rmd, the herein described process can be reproduced and this document can be generated. In the course of this, data from the folder input will be processed and results will be written to output. There are multiple RData files in the folder rdata. They are emitted in the chunks of main.Rmd and saved for a faster process after the first execution. The download stored to input/ignore/pubmed could not be saved in this git repository, because of it's size (1.4 GB). Find out how to get your own version of the xml file below.

GitHub

The code for the herein described process can also be freely downloaded from https://github.com/srfdata/2019-02-clinical-trials.

License

Creative Commons Lizenzvertrag
2019-02-clinical-trials by SRF Data is licensed under a Creative Commons Namensnennung - Attribution ShareAlike 4.0 International License.

Data description of output files

trials.csv

Attribute Type Description
unique_id String Unique identifier assigned by SRF
primary String Trial identification number
size Numeric Number of people participating in study (total, world wide)
study_type Factor Type of study, either Interventional or Observational
status Factor Status of the trial, either Completed, Ongoing, Terminated or Unknown
primary_sponsor String The primary sponsor of the trial (responsible for updating register information)
leading_institution String The (scientifically) leading institution of the trial
registration_date Date Date the trial was registered in the registry
start_date Date Date on which the enrollment process started
end_date Date Date on which the enrollment process ended
results_submitted Boolean Equals true if a result was submitted to the trial registry
publication_found Boolean Equals true if the trial ID was found in cochrane / pubmed
source Factor Shows in which registry this trial was found, either NCT, EUCTR or DRKS
has_g_scholar_results Boolean Equals true if google scholar returned any results when queried with the trial id
primary_sponsor_simple String Simplified Name of primary sponsor (mainly done for swiss institutions)
leading_institution_simple String Simplified Name of leading institution (mainly done for swiss institutions)

Procedure

On the flow chart below, we describe how we tried to find all trials related to Switzerland and how we evaluated whether a publication for that trial exitsts.

Data sources

Trials

We searched the following registers by selecting Switzerland OR Schweiz as a country of recruitement:

WHO (ICTRP)

http://apps.who.int/trialsearch/AdvSearch.aspx

Downloaded 01/14/2019 at 12:35 CET by setting recruitment status to ALL and chosing Export all trials to XML.

ClinicalTrials.gov

https://clinicaltrials.gov/ct2/results?cond=&term=Switzerland&cntry=&state=&city=&dist=

Downloaded 01/14/2019 at 12:31 CET via Download > For Advanced Users: Full Study Record XML Download.

Deutsches Register Klinischer Studien (DRKS)

https://www.drks.de/drks_web/navigate.do?navigationId=search&reset=true

Downloaded 01/24/2019 at 13:20 CET as csv.

Publications

Pubmed

You can query PubMed for all publications with a linked NCT ClinicalTrials.gov ID:

https://www.ncbi.nlm.nih.gov/pubmed/?cmd=Search&term=clinicaltrials.gov%5bsi%5d

We also search the following terms and saved the result as xml by choosing Send to > File > XML:

  • EUDRACT*
  • EUCTR*
  • NCT0*
  • DRKS*

https://www.ncbi.nlm.nih.gov/pubmed?term=(((EUDRACT*)%20OR%20EUCTR*)%20OR%20NCT0*)%20OR%20DRKS*

Downloaded 01/14/2019 at 10:56 CET.

You can read more about finding results of studies on ClinicalTrials.gov.

Cochrane

http://cochranelibrary-wiley.com/cochranelibrary/search?searchRow.searchOptions.searchProducts=clinicalTrialsDoi

Downloaded 01/14/2019 at 10:25 CET by searching ID wildcards e.g. *NCT0* in ti, ab, kw (Title, Abstract, Keywords).

Limit the years to get the total number of trials below the export limit of 20k.

Search terms:

  • NCT0*
  • EUCTR*
  • EUDRACT*
  • Switzerland

Read more about the Cochrane CENTRAL database here.

Kofam/BASEC

The swiss registry for trials is only a secondary register. All the trials in it must also be registered in one of the primary registers (European, German, American registers). It does not contain any information about whether a trial was started or completed.

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