DOI: 10.7910/dvn/6fmtt3
title: Evolution of Reporting P Values in the Biomedical Literature, 1990-2015
title: From JAMA. 2016;315(11) Chavalarias, D., Wallach J. D., Ting Li A. H., Ioannidis J. P. A.

description: &lt;h3&gt;Original dataset from the paper :&lt;/h3&gt;
Chavalarias, D., Wallach, J.D., Li, A.H.T., Ioannidis, J.P.A., 2016. Evolution of Reporting P Values in the Biomedical Literature, 1990-2015. JAMA 315, 1141. doi:10.1001/jama.2016.1952
&lt;br/&gt;
This dataset contains 4,572,043 P values in 1,608,736 Pubmed abstracts and 3,438,299 P values in 385,393 PMC full-text articles extracted from the entire Pubmed 1990-2015 and PMC sample. 
&lt;br/&gt;
&lt;br/&gt;
The dataset of the manual analysis of 1000 abstracts and 100 full texts are also included (named Pval_April_2016.tab).
description: P-value Biomed 1990-2015
description: <b>This dataset contains several sql tables:</b><br>

medline_full_txt_list : the list of all PMC papers analysed with mention of presence of abstract (abs=1), P-values in full text (pv=1), P-value in abstract (pv_abs=1). 
 medline_full_txt_pv : list of PMC P-values extracted in the PMC sample 
 medline_pt : list of P-values extracted in Medline abstracts with PT tags. 


The extracted P-values are stored into a database with the following context details:

 The publication date of the papers associated to the abstract mentioning the P value
 The sign mentioned in the expression : &lt;, &lt;=, &lt;&lt;, ≤ , =, &gt;=, &gt;, &gt;&gt;,≥ or 'less than', 'of &lt;'
 The format of the P-value notation used, distinguishing between the following formats:

 plain : 0,012 or 0.012 or .012
 percentage : 1,2%
 10exp - any form of power of ten: 1,2.10-2, 1,2 x10(-2), 1,2 x10.Exp-2, etc.
 exp - any notation involving 'e', 'E', 'exp' or 'Exp', without mention of the number 10 : 1,2.exp-2, 1.2 x Exp(-2), etc.
 .int – any notation that seems to have a typo, like p=00001.

 The Medline subset and category from which the abstract belongs to. When there were no
references to any subset, the abstract and associated P values were flagged with 'No',
 The journal ID of the paper,


Mysql was used for 'flat' storage and not for its relational properties. Since a given PMID can have several flag or PT or SB associated, the column 'first' indicates for each P-value record the first record of that P-value (first=1) and the other records (first=2). Other values of 'first' column indicates the maximal and minimal P-values at the item level. 

<b>For example :</b>

 "SELECT * FROM `medline_full_txt_pv` WHERE first=1 and DP=1998" will select all P-values from 1998 without duplicate (but if 0.05 appears several times in a PMID, it will have several rows).
 "SELECT * FROM `medline_full_txt_pv` WHERE flag='Research Support' " will select all P-values from the 'Research Support' category without duplicate (but if 0.05 appears several times in a PMID, it will have several rows).


<b>After import of the sql you should have</b>

 1,985,670 rows for the table `medline_full_txt_list`
 12,436,631 rows for the table `medline_full_txt_pv`
 16,116,061 rows for the table `medline_pt`
 9,088,701 rows for the table `medline_pvalues` 


<b>CSV export of all P-values and related meta-data</b>
All P-values and related meta-data have been exported without redundancy (one P-value appears exactly once) in three CSV files:

 <b>List of all PMC items processed. </b>CSV of 843,884 lines corresponding the export of SELECT PMID, PMCID, DP, abs, pv, pv_abs, in_medline_sample, JID, ref FROM `medline_full_txt_list` WHERE FIRST =1
 <b>List of all PMC P-values.</b> CSV of 3,438,299 lines corresponding the export of SELECT PMID, JID, sign, value, DP, format, abs FROM `medline_full_txt_pv` WHERE FIRST =1
 <b>List of all Medline P-values.</b> CSV of 4,572,043 lines corresponding the export of SELECT sign, value, format, DP, JID, PMID, in_pmc_sample FROM `medline_pt` WHERE FIRST =1


<br><br>
The manual analysis of 1000 abstracts and 100 full texts is also included (named Pval_April_2016.tab). It contains :

Sheet 2: Journal Info Information about the 1000 abstracts: Journal
Sheet 3: Extractions_1000 All extractions are based on the abstract only level information. This means that for articles that report data: reviewers felt that reporting of P values of effects in the full text could not be excluded This means that for study design: Decions were based on abstract only Animal or human clarifications: Health policy were generally considered human, "organs" are either human or animal depending on the type of study, genes could be human or animal. If the article was about a technique on humans then it is human. Methods: Lab methods, statistical methods, scientific methods, diverse method based papers
 Sheet 4: Extractions_Data_796 This means that for articles that report data: reviewers felt that reporting of P values of effects in the full text could not be excluded
Sheet 5: Full Text Real Random sample of 100 full text articles with data. Field of study now based on full text.