analysis of pancreas studies started

BibliographicStudies.Rmd

@@ -66,6 +66,11 @@ In this analysis we aimed to identify the common research topics Turkish patholo
 [MeSH Terms Pathology Articles From Turkey](https://sbalci.github.io/pubmed/MeSH_Terms_Pathology_Articles_From_Turkey.html)
 
 
+---
+
+<!-- Pancreas Studies -->
+
+
 ---
 
 <!-- BalciS -->
@@ -116,6 +121,11 @@ In this analysis we aimed to identify the common research topics Turkish patholo
 <!-- pubmedden doi'leri al, doi listesi ile crossref tarat -->
 
 
+---
+
+<!-- USCAP Abstracts vs Published Articles -->
+
+
 ---
 
 <!-- CiteSpaceV -->

PancreasStudies.Rmd

@@ -0,0 +1,254 @@
+---
+title: "Pancreas Studies in Various Bibliometric Tools"
+subtitle: "Pancreas Studies in Pathology Journals"
+author: "Serdar Balcı, MD, Pathologist"
+date: '`r format(Sys.Date())`'
+output: 
+  html_notebook: 
+    code_folding: hide
+    fig_caption: yes
+    highlight: monochrome
+    number_sections: yes
+    theme: paper
+    toc: yes
+    toc_depth: 5
+    toc_float: yes
+---
+
+<!-- Open all links in new tab-->  
+<!-- <base target="_blank"/>    -->
+
+
+<!-- Go to www.addthis.com/dashboard to customize your tools --> <script type="text/javascript" src="//s7.addthis.com/js/300/addthis_widget.js#pubid=ra-5bc36900a405090b">  
+</script> 
+
+
+```{r global_options, include=FALSE}
+knitr::opts_chunk$set(fig.width = 12, fig.height = 8, 
+                      # fig.path = 'figures/',
+                      echo = FALSE, warning = FALSE, message = FALSE, error = FALSE, eval = TRUE, tidy = TRUE, comment = NA)
+```
+
+```{r library, include=FALSE}
+library(tidyverse)
+```
+
+
+
+
+# Introduction
+
+- Selected Pathology Journals are used for the query^[[Selected Pathology Journals](PancreasStudies/data/journal_list_from_my_collections)]
+
+
+
+
+# PubMed
+
+## Data Download from PubMed via EDirect
+
+- Data is downloaded from PubMed via Edirect^[https://dataguide.nlm.nih.gov/edirect/overview.html]
+
+- 
+
+
+## rentrez
+
+# europepmc
+
+
+
+# WOS
+
+[WOS.Rmd](WOS.Rmd)
+
+```{r}
+PMID_List_for_WOS_pancreas <- paste0("PMID=(", pmid_only_path_journals$PMID, ") OR")
+
+write(PMID_List_for_WOS_pancreas,
+      here::here("PancreasStudies/data/PMID_List_for_WOS_pancreas.txt")
+)
+
+```
+
+
+
+
+
+
+
+# Scopus
+
+[scopus.Rmd](scopus.Rmd)
+
+
+# Vosviewer
+
+Author Thesaurus is used.^[[Author Thesaurus](data/thesaurus_authors.txt)]
+
+Code for interactive graph.^[[Interactive Graph Code](data/VOSviewer_interactive_graphcode.txt)]
+
+
+
+
+
+
+# Cite Space
+
+# CitNetExplorer
+
+# Lens
+
+```
+(citation_id_type: "pmid"  AND citation_id: 28984336)  OR (citation_id_type: "pmid"  AND citation_id: 21682559)
+```
+
+```{r}
+pmid_only_path_journals <- 
+read_delim("PancreasStudies/data/pmid_only_path_journals.txt", "\n", col_names = "PMID", col_types = "c")
+
+pmid_only_path_journals2 <- paste0("(citation_id_type: 'pmid'  AND citation_id:",pmid_only_path_journals$PMID, ") OR ", collapse = "")
+
+write(pmid_only_path_journals2,
+"PancreasStudies/data/lensSearch.txt"
+)
+```
+
+
+
+
+# openknowledgemaps
+
+Open Knowledge Maps (2019). Overview of research on intraductal tubulopapillary neoplasm. Retrieved from https://openknowledgemaps.org/map/cc04c53301920a93d451aa2ce3010243/ [30 Mar 2019]. 
+
+
+# bibliometrix
+
+# ORCID
+
+# Semantic Scholar
+
+[SemanticScholar.Rmd](SemanticScholar.Rmd)
+
+
+# Microsoft Academic
+
+# Scopus
+
+# Altmetrics
+
+
+
+# Grid
+
+https://grid.ac/
+
+
+# ROR
+
+https://ror.org/search?page=1&query=turkey
+
+
+# Cobalmetrics
+
+https://cobaltmetrics.com/
+
+- Toward privacy-preserving altmetrics exploration with Cobaltmetrics and ORCID
+
+https://medium.com/thunken/toward-privacy-preserving-altmetrics-exploration-with-cobaltmetrics-and-orcid-f5ab6fa7898a
+
+
+# OpenCitations
+
+http://opencitations.net
+
+http://opencitations.net/download
+
+http://opencitations.net/corpus
+
+https://github.com/opencitations
+
+- The OpenCitations Data Model  
+https://figshare.com/articles/Metadata_for_the_OpenCitations_Corpus/3443876
+
+- Creating Open Citation Data with BCite  
+https://semsci.github.io/SemSci2018/papers/1/bcite-semsci2018.html
+
+https://github.com/opencitations/bcite
+
+
+# Open Knowledge Maps
+
+Open Knowledge Maps (2019). Overview of research on (pathology[affiliation] or patoloji[affiliation]) and (turkey[affiliation] or türkiye[affiliation]). Retrieved from https://openknowledgemaps.org/map/e4dbf6c89015e402d6d7d560ab79e17a/ [30 Mar 2019]. 
+
+
+https://openknowledgemaps.org/index
+
+
+
+# iris.ai
+
+https://the.iris.ai/map/02f89d24-0415-43ab-878a-853ec17c5a59
+
+# lens.org
+
+https://www.lens.org/lens/scholar/search/results?dateFilterField=year_published&filterMap=%7B%7D&orcids=0000-0002-7852-3851&orderBy=%2Bpublished&preview=true&previewType=SCHOLAR_ANALYSIS&regexEnabled=false
+
+https://www.lens.org/lens/scholar/search/results?q=(author.affiliation.name:%20%22pathology%22%20%20OR%20author.affiliation.name:%20%22patoloji%22)%20%20AND%20(author.affiliation.name:%20%22Turkey%22%20%20OR%20author.affiliation.name:%20%22T%C3%BCrkiye%22)
+
+https://www.lens.org/lens/scholar/search/analysis?q=(author.affiliation.name:%20%22neurosurgery%22%20%20OR%20author.affiliation.name:%20%22sport%22%20)%20AND%20(abstract:%20%22sport%22%20%20OR%20title:%20%22sport%22)&page=0&limit=10&orderBy=%2Bscore&dateFilterField=year_published&preview=false&regexEnabled=false
+
+
+# To Do
+
+- find a way to auto import journal names
+- remove last OR
+- Auto run posiible analysis via cron
+- Find a way to auto copy into googledrive
+- push to blog, netlify ...
+- Add from
+-- [Sources.Rmd](Sources.Rmd)  
+-- [Bibliyometri.Rmd](Bibliyometri.Rmd)  
+
+
+
+
+# About & 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()`.
+
+---
+
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+---
+
+# References
+
+
+
+