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Sources.Rmd
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Sources.Rmd
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---
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:
code_folding: hide
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®exEnabled=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®exEnabled=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