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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.

# Introduction

These studies require too much effort, since the data is generally behind paywalls and restrictions.
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.
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
I will be using the following;
<!-- list of analysis tools -->
[R Markdown](https://rmarkdown.rstudio.com/)
,
Expand All @@ -57,203 +56,191 @@ and
[Google Scholar](https://scholar.google.com).


http://opencitations.net/download
---



https://www.scopus.com/sources


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



https://dtd.nlm.nih.gov/ncbi/pubmed/out/doc/2018/
# Codes for data download

## PubMed

MEDLINE®PubMed® XML Element Descriptions and their Attributes
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
- Comment Correction Type
https://www.ncbi.nlm.nih.gov/books/NBK3827/#pubmedhelp.Comment_Correction_Type

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

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/

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

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

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

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

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

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

Using EDirect to create a local copy of PubMed
https://dataguide.nlm.nih.gov/edirect/archive.html

EDirectCookbook
https://ncbi-hackathons.github.io/EDirectCookbook/
### Entrez Direct: E-utilities on the UNIX Command Line

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/

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

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

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


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

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.
- Using EDirect to create a local copy of PubMed

---
https://dataguide.nlm.nih.gov/edirect/archive.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()`.

---
```
https://dataguide.nlm.nih.gov/edirect/archive.html
archive-pubmed -path /Volumes/Agu2018/PubMed
---
title: "Bibliographic Studies"
subtitle: "Sources Used For Analysis"
author: "Serdar Balcı, MD, Pathologist"
date: '`r format(Sys.Date())`'
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
---
caffeinate
# Introduction
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
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.
esearch -db pubmed -query "Turkey[Affiliation]" \
-datetype PDAT -mindate 2018 -maxdate 3000 | \
efetch -format xml > data/Turkey_all2.xml
```

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

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

In order to automatize these type of analysis in a reproducable fashion,
I will be using
<!-- 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/).
http://titipata.github.io/pubmed_parser/
http://github.com/titipata/pubmed_parser

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).

### MEDLINEXMLToJSON

https://github.com/ldbib/MEDLINEXMLToJSON

https://www.scopus.com/sources

### Workflow of Pubmed Parser with PySpark

https://www.altmetric.com/top100/2018/
https://github.com/titipata/pubmed_parser/wiki


https://grid.ac/

## ORCID

https://dtd.nlm.nih.gov/ncbi/pubmed/out/doc/2018/
https://orcid.org/content/orcid-public-data-file

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

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

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

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
## Semantic Scholar

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

EDirect Documentation
https://dataguide.nlm.nih.gov/edirect/documentation.html
```
Semantic Scholar Open Research Corpus
NCBI NOW, Lecture 3, Introduction to the Linux Shell
https://www.youtube.com/watch?v=XgaE4VIaJqI
https://s3-us-west-2.amazonaws.com/ai2-s2-research-public/open-corpus/index.html
MEDLINE®/PubMed® XML Data Elements
https://www.nlm.nih.gov/bsd/licensee/data_elements_doc.html
aws s3 cp --recursive s3://ai2-s2-research-public/open-corpus/ ~/Volumes/Agu2018/semantic/
pubmed_180101.dtd Documentation
https://dtd.nlm.nih.gov/ncbi/pubmed/out/doc/2018/
wget -P /Volumes/Agu2018/semantic -i https://s3-us-west-2.amazonaws.com/ai2-s2-research-public/open-corpus/manifest.txt
Using EDirect to create a local copy of PubMed
https://dataguide.nlm.nih.gov/edirect/archive.html
caffeinate
EDirectCookbook
https://ncbi-hackathons.github.io/EDirectCookbook/
```

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

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

Installing EDirect
https://dataguide.nlm.nih.gov/edirect/install.html
https://www.scopus.com/sources


---

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.
## Altmetrics

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


## Grid

https://grid.ac/



## 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


---

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This document will be continiously updated and the last update was on `r Sys.Date()`.

---
---

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