-
Notifications
You must be signed in to change notification settings - Fork 0
/
BibliographicStudies.Rmd
381 lines (238 loc) · 11.1 KB
/
BibliographicStudies.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
---
title: "Bibliometric Studies"
subtitle: "Reproducible Bibliometric Analysis of Pathology Articles Using PubMed, E-direct, WoS, Google Scholar"
author: "Serdar Balcı, MD, Pathologist"
date: '`r format(Sys.Date())`'
bibliography: bib/BibliographicStudies.bib
output:
html_notebook:
code_folding: hide
fig_caption: yes
highlight: kate
number_sections: yes
theme: cerulean
toc: yes
toc_depth: 5
toc_float: yes
html_document:
code_folding: hide
df_print: kable
highlight: kate
keep_md: yes
number_sections: yes
theme: cerulean
toc: yes
toc_float: yes
---
<a class="twitter-follow-button" data-show-count="false"
href="https://twitter.com/serdarbalci">Follow @serdarbalci</a><script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
[![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat)](https://github.com/sbalci/PubMed/issues)
[![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg)](https://saythanks.io/to/sbalci)
[![HitCount](http://hits.dwyl.io/sbalci/PubMed.svg)](http://hits.dwyl.io/sbalci/PubMed)
# Introduction
It is a very common bibliometric study type to retrospectively analyse the number of peer reviewed articles written from a country to view the amount of contribution made in a specific scientific discipline.
These studies require too much effort, since the data is generally behind paywalls and restrictions.
I have previously contributed to a research to identify the Articles from Turkey Published in Pathology Journals Indexed in International Indexes; which is published here: [Turk Patoloji Derg. 2010, 26(2):107-113 doi: 10.5146/tjpath.2010.01006](http://www.turkjpath.org/summary_en.php3?id=1423)
This study had required manual investigation of many excel files, which was time consuming; also redoing and updating the data and results require a similar amount of effort.
---
If you want to see the code used in the analysis please click the code button on the right upper corner or throughout the page.
I would like to hear your feedback: https://goo.gl/forms/YjGZ5DHgtPlR1RnB3
This document will be continiously updated and the last update was on `r Sys.Date()`.
---
# Analysis
---
## Country Based Comparison
To see the analysis comparing number of pathology articles from Turkey, German and Japan see this analysis: [Country Based Comparison](https://sbalci.github.io/pubmed/CountryBasedComparison.html)
---
## Articles per Journals per Country
In this analysis we aimed to compare number articles per journals per country. We tried to identify if articles from a country is published in certain journals: [Articles Per Journals Per Country](https://sbalci.github.io/pubmed/ArticlesPerJournalsPerCountry.html)
## Most Common MeSH Terms and Keywords used in Pathology Articles from Turkey
In this analysis we aimed to identify the common research topics Turkish pathologists are interested. We extracted most common MeSH terms and keywords from PubMed articles using EDirect:
[MeSH Terms Pathology Articles From Turkey](https://sbalci.github.io/pubmed/MeSH_Terms_Pathology_Articles_From_Turkey.html)
---
## Pancreas Studies with Various Bibliometric Tools - Pancreas Studies in Pathology Journals
[Pancreas Studies with Various Bibliometric Tools - Pancreas Studies in Pathology Journals](PancreasStudies.nb.html)
---
<!-- BalciS -->
---
<!-- ## Journals Published Articles From Turkey -->
---
<!-- ## SEER Research Per Countries / Who is doing SEER Research? -->
---
<!-- ## Semantic Scholar -->
---
<!-- ## neutrophil lymph ratio -->
---
<!-- ## retracted pathology articles -->
---
<!-- ## correction pathology articles -->
---
<!-- ## p values in pathology articles a text analysis of pubmed articles using regular expression -->
---
<!-- ## ulakbim patoloji TR dizin -->
---
<!-- ## europepmc paketi ile endometriozis analizi -->
---
<!-- VOSviewer için -->
<!-- pubmedden doi'leri al, doi listesi ile crossref tarat -->
---
<!-- USCAP Abstracts vs Published Articles -->
---
<!-- CiteSpaceV -->
<!-- CitNetExplorer -->
<!-- CodeForGitHubGist -->
<!-- css -->
<!-- data -->
<!-- docs -->
<!-- e-utilities-lecture-notes -->
<!-- figure -->
<!-- grid-2018-11-14 -->
<!-- images -->
<!-- Neurosurgery-Articles -->
<!-- pdf -->
<!-- Pediatric-Surgery -->
<!-- rsconnect -->
<!-- Videos -->
<!-- VOSviewer -->
<!-- ArticlesPerJournalsPerCountry.nb.html -->
<!-- BibliographicStudies.html -->
<!-- BibliographicStudies.nb.html -->
<!-- CountryBasedComparison.nb.html -->
<!-- endometriosis.nb.html -->
<!-- JournalsPublishedArticlesFromTurkey.nb.html -->
<!-- Making proper trend graphs.htm -->
<!-- MeSH_Terms_Pathology_Articles_From_Turkey.nb.html -->
<!-- p-values-in-Pathology-Articles.nb.html -->
<!-- PathologyArticlesFromTurkeyComparedtoAllPublishedArticles.nb.html -->
<!-- PubMedPackages.nb.html -->
<!-- README.html -->
<!-- Retrieving and Processing PubMed Records via easyPubMed (html).htm -->
<!-- SchedulePubMedAnalysis.nb.html -->
<!-- SchedulePubMedAnalysis2.nb.html -->
<!-- SEERResearchPerCountries.nb.html -->
<!-- SemanticScholar.nb.html -->
<!-- Sources.html -->
<!-- Sources.nb.html -->
<!-- Untitled.nb.html -->
---
# Sources Used For Analysis
Here are the sources used in these analysis: [Sources Used For Analysis](https://sbalci.github.io/pubmed/Sources.html)
---
# Feedback
[Serdar Balcı, MD, Pathologist](https://github.com/sbalci) would like to hear your feedback: https://goo.gl/forms/YjGZ5DHgtPlR1RnB3
This document will be continiously updated and the last update was on `r Sys.Date()`.
---
<script id="dsq-count-scr" src="//https-sbalci-github-io.disqus.com/count.js" async></script>
<div id="disqus_thread"></div>
<script>
/**
* RECOMMENDED CONFIGURATION VARIABLES: EDIT AND UNCOMMENT THE SECTION BELOW TO INSERT DYNAMIC VALUES FROM YOUR PLATFORM OR CMS.
* LEARN WHY DEFINING THESE VARIABLES IS IMPORTANT: https://disqus.com/admin/universalcode/#configuration-variables*/
/*
var disqus_config = function () {
this.page.url = PAGE_URL; // Replace PAGE_URL with your page's canonical URL variable
this.page.identifier = PAGE_IDENTIFIER; // Replace PAGE_IDENTIFIER with your page's unique identifier variable
};
*/
(function() { // DON'T EDIT BELOW THIS LINE
var d = document, s = d.createElement('script');
s.src = 'https://https-sbalci-github-io.disqus.com/embed.js';
s.setAttribute('data-timestamp', +new Date());
(d.head || d.body).appendChild(s);
})();
</script>
<noscript>Please enable JavaScript to view the <a href="https://disqus.com/?ref_noscript">comments powered by Disqus.</a></noscript>
---
---
title: "Bibliographic Studies"
subtitle: "Reproducible Bibliometric Analysis of Pathology Articles Using PubMed, E-direct, WoS, Google Scholar"
author: "Serdar Balcı, MD, Pathologist"
date: '`r format(Sys.Date())`'
output:
html_document:
code_folding: hide
df_print: kable
highlight: kate
keep_md: yes
number_sections: yes
theme: cerulean
toc: yes
toc_float: yes
html_notebook:
code_folding: hide
fig_caption: yes
highlight: kate
number_sections: yes
theme: cerulean
toc: yes
toc_depth: 5
toc_float: yes
---
# Introduction
It is a very common bibliometric study type to retrospectively analyse the number of peer reviewed articles written from a country to view the amount of contribution made in a specific scientific discipline.
These studies require too much effort, since the data is generally behind paywalls and restrictions.
I have previously contributed to a research to identify the Articles from Turkey Published in Pathology Journals Indexed in International Indexes; which is published here: [Turk Patoloji Derg. 2010, 26(2):107-113 doi: 10.5146/tjpath.2010.01006](http://www.turkjpath.org/summary_en.php3?id=1423)
This study had required manual investigation of many excel files, which was time consuming; also redoing and updating the data and results require a similar amount of effort.
---
If you want to see the code used in the analysis please click the code button on the right upper corner or throughout the page.
I would like to hear your feedback: https://goo.gl/forms/YjGZ5DHgtPlR1RnB3
This document will be continiously updated and the last update was on `r Sys.Date()`.
---
# Analysis
---
## Country Based Comparison
To see the analysis comparing number of pathology articles from Turkey, German and Japan see this analysis: [Country Based Comparison](https://sbalci.github.io/pubmed/CountryBasedComparison.html)
---
## Articles per Journals per Country
In this analysis we aimed to compare number articles per journals per country. We tried to identify if articles from a country is published in certain journals: [Articles Per Journals Per Country](https://sbalci.github.io/pubmed/ArticlesPerJournalsPerCountry.html)
## Most Common MeSH Terms and Keywords used in Pathology Articles from Turkey
In this analysis we aimed to identify the common research topics Turkish pathologists are interested. We extracted most common MeSH terms and keywords from PubMed articles using EDirect:
[MeSH Terms Pathology Articles From Turkey](https://sbalci.github.io/pubmed/MeSH_Terms_Pathology_Articles_From_Turkey.html)
---
<!-- ## Journals Published Articles From Turkey -->
---
<!-- ## SEER Research Per Countries / Who is doing SEER Research? -->
---
<!-- ## Semantic Scholar -->
---
<!-- ## neutrophil lymph ratio -->
---
## retracted pathology articles
retraction, correction and republication in pathology journals
RetractedPathologyArticles.nb.html
---
<!-- ## p values in pathology articles a text analysis of pubmed articles using regular expression -->
---
<!-- ## ulakbim patoloji TR dizin -->
---
## europepmc paketi ile endometriozis analizi
endometriosis.nb.html
---
# Sources Used For Analysis
Here are the sources used in these analysis: [Sources Used For Analysis](https://sbalci.github.io/pubmed/Sources.html)
---
# Feedback
[Serdar Balcı, MD, Pathologist](https://github.com/sbalci) would like to hear your feedback: https://goo.gl/forms/YjGZ5DHgtPlR1RnB3
This document will be continiously updated and the last update was on `r Sys.Date()`.
---
<script id="dsq-count-scr" src="//https-sbalci-github-io.disqus.com/count.js" async></script>
<div id="disqus_thread"></div>
<script>
/**
* RECOMMENDED CONFIGURATION VARIABLES: EDIT AND UNCOMMENT THE SECTION BELOW TO INSERT DYNAMIC VALUES FROM YOUR PLATFORM OR CMS.
* LEARN WHY DEFINING THESE VARIABLES IS IMPORTANT: https://disqus.com/admin/universalcode/#configuration-variables*/
/*
var disqus_config = function () {
this.page.url = PAGE_URL; // Replace PAGE_URL with your page's canonical URL variable
this.page.identifier = PAGE_IDENTIFIER; // Replace PAGE_IDENTIFIER with your page's unique identifier variable
};
*/
(function() { // DON'T EDIT BELOW THIS LINE
var d = document, s = d.createElement('script');
s.src = 'https://https-sbalci-github-io.disqus.com/embed.js';
s.setAttribute('data-timestamp', +new Date());
(d.head || d.body).appendChild(s);
})();
</script>
<noscript>Please enable JavaScript to view the <a href="https://disqus.com/?ref_noscript">comments powered by Disqus.</a></noscript>
---