Sources.Rmd

---
title: "Bibliographic Studies"
subtitle: "Sources Used For Analysis"
author: "Serdar Balcı, MD, Pathologist"
date: '`r format(Sys.Date())`'
bibliography: bib/sources.bib
output: 
  html_notebook: 
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    fig_caption: yes
    highlight: kate
    number_sections: yes
    theme: cerulean
    toc: yes
    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
---


# 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.

In order to automatize these type of analysis in a reproducable fashion, 
I will be using the following;  
<!-- list of analysis tools -->
[R Markdown](https://rmarkdown.rstudio.com/)
,
[R Notebook](https://rmarkdown.rstudio.com/r_notebooks.html)
,
[Shiny](https://shiny.rstudio.com/)
and
[Terminal](https://en.0wikipedia.org/wiki/Terminal_(macOS))
for coding. 
I also plan to use other bibliographic tools like
[VOSviewer](http://www.vosviewer.com/).

Data will be retrieved from 
[PubMed](https://www.ncbi.nlm.nih.gov/pubmed), 
[E-direct](https://dataguide.nlm.nih.gov/edirect/overview.html),
[WoS](www.webofknowledge.com/)
and
[Google Scholar](https://scholar.google.com).


---


# Codes for data download

## PubMed

https://dtd.nlm.nih.gov/ncbi/pubmed/out/doc/2018/

- MEDLINE®PubMed® XML Element Descriptions and their Attributes
https://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html

- Comment Correction Type
https://www.ncbi.nlm.nih.gov/books/NBK3827/#pubmedhelp.Comment_Correction_Type

- EDirect Documentation
https://dataguide.nlm.nih.gov/edirect/documentation.html

- Entrez Direct: E-utilities on the UNIX Command Line
https://www.ncbi.nlm.nih.gov/books/NBK179288/

- The 9 E-utilities and Associated Parameters
https://dataguide.nlm.nih.gov/eutilities/utilities.html

- E-utilities and the History server
https://dataguide.nlm.nih.gov/eutilities/history.html

- EDirect Documentation
https://dataguide.nlm.nih.gov/edirect/documentation.html

- NCBI NOW, Lecture 3, Introduction to the Linux Shell
https://www.youtube.com/watch?v=XgaE4VIaJqI

- MEDLINE®/PubMed® XML Data Elements
https://www.nlm.nih.gov/bsd/licensee/data_elements_doc.html

- pubmed_180101.dtd Documentation
https://dtd.nlm.nih.gov/ncbi/pubmed/out/doc/2018/


### Edirect docker

- Official NCBI EDirect docker image

https://github.com/ncbi/docker/tree/master/edirect

- ncbi-docker

https://github.com/ncbi/docker

- NCBI EDirect Docker image

https://hub.docker.com/r/ncbi/edirect

`docker pull ncbi/edirect`




### edirect anaconda

https://anaconda.org/bioconda/repo

https://anaconda.org/bioconda/entrez-direct

`conda install -c bioconda entrez-direct`








### Entrez Direct: E-utilities on the UNIX Command Line

- Entrez Direct: E-utilities on the UNIX Command Line  
https://www.ncbi.nlm.nih.gov/books/NBK179288/

- EDirectCookbook
https://ncbi-hackathons.github.io/EDirectCookbook/

- EDirect Overview
https://dataguide.nlm.nih.gov/edirect/overview.html

- Installing EDirect
https://dataguide.nlm.nih.gov/edirect/install.html


### Using EDirect to create a local copy of PubMed

- Using EDirect to create a local copy of PubMed  

https://dataguide.nlm.nih.gov/edirect/archive.html




```

https://dataguide.nlm.nih.gov/edirect/archive.html

archive-pubmed -path /Volumes/Agu2018/PubMed

caffeinate

esearch -db pubmed -query "breast cancer" | \
efetch -format uid | \
fetch-pubmed -path /Volumes/Agu2018/PubMed | \
xtract -pattern PubmedArticle -element MedlineCitation/PMID ISOAbbreviation Volume Issue PubDate/Year > trial.txt

esearch -db pubmed -query "Turkey[Affiliation]" \
-datetype PDAT -mindate 2018 -maxdate 3000 | \
efetch -format xml > data/Turkey_all2.xml

```



### Parser for Pubmed Open-Access XML Subset and MEDLINE XML Dataset

- Python XML parser for PubMed Open Access subset and MEDLINE dataset  

http://titipata.github.io/pubmed_parser/  
http://github.com/titipata/pubmed_parser  


### MEDLINEXMLToJSON

https://github.com/ldbib/MEDLINEXMLToJSON


### Workflow of Pubmed Parser with PySpark

https://github.com/titipata/pubmed_parser/wiki

## WOS

## EigenFactor

- EigenFactor Search

http://www.eigenfactor.org/projects/journalRank/journalsearch.php

- Scholarly publications 

http://www.eigenfactor.org/papers.php

- Projects

http://www.eigenfactor.org/projects.php


## ORCID

https://orcid.org/content/orcid-public-data-file

https://orcid.org/blog/2019/01/11/free-everyone-always-orcid-public-api-and-data-file


- A compendium of taxonomists on ORCID  
https://orcid.org/blog/2018/04/06/compendium-taxonomists-orcid

- Vast set of public CVs reveals the world’s most migratory scientists  
https://www.sciencemag.org/news/2017/05/vast-set-public-cvs-reveals-world-s-most-migratory-scientists


## Semantic Scholar

https://www.semanticscholar.org/


### Semantic Scholar Open Research Corpus

```
Semantic Scholar Open Research Corpus

https://s3-us-west-2.amazonaws.com/ai2-s2-research-public/open-corpus/index.html

aws s3 cp --recursive s3://ai2-s2-research-public/open-corpus/ ~/Volumes/Agu2018/semantic/

wget -P /Volumes/Agu2018/semantic -i https://s3-us-west-2.amazonaws.com/ai2-s2-research-public/open-corpus/manifest.txt

caffeinate

```



### AllenNLP

https://allennlp.org/


### An open-source NLP research library, built on PyTorch.

http://www.allennlp.org/

https://github.com/allenai/allennlp


### citeomatic

https://allenai.org/semantic-scholar/citeomatic/


### an error

https://www.semanticscholar.org/paper/PBPath-Journal-Watch/46b65ddf9128eed990f938d1db7a1f1473b4c7c9

https://pdfs.semanticscholar.org/46b6/5ddf9128eed990f938d1db7a1f1473b4c7c9.pdf?_ga=2.114635586.411458507.1562087790-426299917.1562087790




## Microsoft Academic

https://labs.cognitive.microsoft.com/en-us/project-academic-knowledge

https://academic.microsoft.com/author/2608586067/publication/search?q=Serdar%20Balci

## Scopus

https://www.scopus.com/sources



## Altmetrics

https://www.altmetric.com/top100/2018/


## 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


## contentmine

http://contentmine.org/

https://github.com/ContentMine



## lens.org


<iframe src="https://player.vimeo.com/video/295099740" width="640" height="360" frameborder="0" webkitallowfullscreen mozallowfullscreen allowfullscreen></iframe>
<p><a href="https://vimeo.com/295099740">The Lens</a> from <a href="https://vimeo.com/user10734565">Cambia</a> on <a href="https://vimeo.com">Vimeo</a>.</p>


<iframe src="https://player.vimeo.com/video/245867897" width="640" height="360" frameborder="0" allowfullscreen></iframe>

<iframe src="https://player.vimeo.com/video/246041050" width="640" height="360" frameborder="0" allowfullscreen></iframe>

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


```
my_data_frame <- readr::read_delim("~/downloads/pubmed_result.txt", delim = "\t", col_names = FALSE)

chunk <- 5000
mylist <-  split(my_data_frame, rep(1:ceiling(nrow(my_data_frame)/chunk), each=chunk, length.out=nrow(my_data_frame)))

X1 <- mylist$`1`
X2 <- mylist$`2`
X3 <- mylist$`3`
X4 <- mylist$`4`

readr::write_csv(X1, "~/downloads/1.txt")
readr::write_csv(X2, "~/downloads/2.txt")
readr::write_csv(X3, "~/downloads/3.txt")
readr::write_csv(X4, "~/downloads/4.txt")

```




#### PatCite


## Apache UIMA

Unstructured Information Management applications

https://uima.apache.org/index.html

---

## EuropePMC

- Tools overview

https://europepmc.org/tools

- Developer resources

https://europepmc.org/developers

- Articles RESTful API

https://europepmc.org/RestfulWebService

- Grants RESTful (Grist) API

https://europepmc.org/GristAPI

- SOAP web service

https://europepmc.org/SoapWebServices

- Europe PMC Annotations API

https://europepmc.org/AnnotationsApi

- OAI service

https://europepmc.org/OaiService

- Bulk downloads

https://europepmc.org/downloads



---

## ELIXIR Core Data Resources

https://elixir-europe.org/platforms/data/core-data-resources


---

## scite


https://scite.ai/


---

## TÜBİTAK Destekli Projeler Veri Tabanı

Ülkemizdeki araştırma altyapısına katkı sağlamak amacıyla, Araştırma Destek Programları Başkanlığı (ARDEB) bünyesinde, 1965 yılından günümüze kadar sonuçlanmış olan 17.808 adet projenin sonuç raporunun tam metinleri, TÜBİTAK Ulusal Akademik Ağ ve Bilgi Merkezi (ULAKBİM) “TÜBİTAK Destekli Projeler Veri Tabanı”nda yayımlanmaktadır.


Söz konusu veri tabanına https://trdizin.gov.tr/search/projectSearch.xhtml linkinden erişim sağlanabilmekte ve sonuç raporlarına ilişkin proje no, başlık, yürütücü/araştırmacı/danışman adı, yıl ve anahtar kelime bazında tarama yapılabilmektedir.


## TRDizin

https://trdizin.gov.tr/


## bioRxiv API 


http://api.biorxiv.org/


http://api.biorxiv.org/reports/



---

# Software


## R-project

https://github.com/schochastics/graphlayouts


### rentrez

```
https://github.com/ropensci/rentrez/issues/134#event-2313355730

library(rentrez)
library(XML)

MeSH_from_pmid <- function(pmid){
   rec <- entrez_fetch(db="pubmed", id=pmid, rettype = "xml", parsed=TRUE)
   m_names <- xpathSApply(rec, "//MeshHeadingList/MeshHeading/DescriptorName", xmlValue)
   m_ui <- xpathSApply(eg_rec, "//MeshHeadingList/MeshHeading/DescriptorName", xmlAttrs)[1,]
   data.frame(mesh_ui = m_ui, descriptor = m_names)
}

MeSH_from_pmid(27591765)



```



## CiteSpace

- CiteSpace Tutorial

http://cluster.ischool.drexel.edu/~cchen/citespace/tutorial/



---

# Bibliometric Study Examples

- Origins of Life Research: a Bibliometric Approach [@Aydinoglu2018] 

Aydinoglu, A.U. & Taşkın, Z. Orig Life Evol Biosph (2018) 48: 55. https://doi.org/10.1007/s11084-017-9543-4  
https://link.springer.com/article/10.1007/s11084-017-9543-4  

- Yükseköğretim ve Bilim Dergisi

http://higheredu-sci.beun.edu.tr/

- CWTS Blog

https://www.cwts.nl/blog

- Bilgi Dünyası

http://bd.org.tr/index.php/bd

---

# Websites

- Half Life: The Decay of Knowledge and What to Do About It

https://fs.blog/2018/03/half-life/

-  Has the tide turned towards responsible metrics in research? 

https://www.theguardian.com/science/political-science/2018/jul/10/has-the-tide-turned-towards-responsible-metrics-in-research

- Ahlaksız büyüme 

https://blog.metu.edu.tr/akcomak/2013/06/13/ahlaksiz-buyume-2/



---

# Organisations of Bibliometrics  

- University Ranking by Academic Performance  

URAP  
http://www.urapcenter.org/2018/index.php  

URAP Turkey  
http://tr.urapcenter.org/2018/  

- https://gate.ac.uk/

-  Responsible Metrics

https://www.cwts.nl/research/research-themes/responsible-metrics

-  Leiden Manifesto for Research Metrics

http://www.leidenmanifesto.org/

- CWTS Leiden Ranking

http://www.leidenranking.com/


---

# 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