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https://github.com/dvklopfenstein/pmidcite

Turbocharge a PubMed literature rather than clicking and clicking and clicking on Google Scholar
https://github.com/dvklopfenstein/pmidcite
citation-analysis citation-counts citation-downloader citedby command-line-tool library literature-review literature-search ncbi nih-citation-data pmid pubmed snowballing
Last synced: 2 days ago
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Turbocharge a PubMed literature rather than clicking and clicking and clicking on Google Scholar
Host: GitHub
URL: https://github.com/dvklopfenstein/pmidcite
Owner: dvklopfenstein
License: agpl-3.0
Created: 2019-11-22T17:36:34.000Z (about 5 years ago)
Default Branch: main
Last Pushed: 2024-09-30T16:20:39.000Z (3 months ago)
Last Synced: 2024-12-13T06:04:54.876Z (9 days ago)
Topics: citation-analysis, citation-counts, citation-downloader, citedby, command-line-tool, library, literature-review, literature-search, ncbi, nih-citation-data, pmid, pubmed, snowballing
Language: Python
Homepage:
Size: 22.5 MB
Stars: 29
Watchers: 5
Forks: 7
Open Issues: 8
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: docs/CONTRIBUTING.md
- Funding: .github/FUNDING.yml
- License: LICENSE
- Code of conduct: docs/CODE_OF_CONDUCT.md
- Citation: CITATION.cff
Awesome Lists containing this project

README

        # PubMed ID (PMID) Cite

[![Tweet](https://img.shields.io/twitter/url/http/shields.io.svg?style=social)](https://twitter.com/intent/tweet?text=Python%20library%20to%20download%20pubmed%20citation%20counts%20and%20data,%20given%20a%20PMID&url=https://github.com/dvklopfenstein/pmidcite&via=dvklopfenstein&hashtags=pubmed,pmid,citations,pubmed2cite,writingtips,scientificwriting)

[![CodeQL](https://github.com/dvklopfenstein/pmidcite/actions/workflows/codeql-analysis.yml/badge.svg)](https://github.com/dvklopfenstein/pmidcite/actions/workflows/codeql-analysis.yml)

[![Latest PyPI version](https://img.shields.io/pypi/v/pmidcite.svg)](https://pypi.org/project/pmidcite/)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5172712.svg)](https://doi.org/10.5281/zenodo.5172712)



Turbocharge a [**PubMed**](https://pubmed.ncbi.nlm.nih.gov) literature search with the command, `icite`, rather than clicking and clicking and clicking on [**Google Scholar**](/doc/images/README_twitter.md) "*Cited by N*" links.

This open-source project is part of [**a peer-reviewed**](https://pubmed.ncbi.nlm.nih.gov/33031632) [**commentary**](https://onlinelibrary.wiley.com/doi/10.1002/jrsm.1456) that was invited by the editors of [***Research Synthesis Methods***](https://onlinelibrary.wiley.com/journal/17592887).

Please [**Cite**](#how-to-cite) if you use *pmidcite* in your research or literature search.    

Contact: [email protected]     

# PubMed and NIH Citation data

PubMed contains peer-reviewed research papers

in biomedicine, biochemistry, chemistry, behavioral science, and other life sciences.

[**Citation data**](https://icite.od.nih.gov) is downloaded

each time `icite` is run

from the [**National Institutes of Health (NIH)**](https://www.nih.gov/) and includes:

* Citation counts of all papers and clinical papers

* Performance of a paper among its peer papers

* Existence of MeSH terms for the human, animal, and molecular/cellular categories

# Table of Contents

* ***Quickstart on the*** [***command line***](https://github.com/dvklopfenstein/pmidcite/blob/main/README.md#command-line-interface-cli)

  * [**1) Download citation counts and data for a research paper**](https://github.com/dvklopfenstein/pmidcite#1-download-citation-counts-and-data-for-a-research-paper)

  * [**2) Forward citation search**](https://github.com/dvklopfenstein/pmidcite#2-forward-citation-search): following a paper's *Cited by* links or *Forward snowballing*

  * [**3) Backward citation search**](https://github.com/dvklopfenstein/pmidcite#3-backward-citation-search): following the links to a paper's references or *Backward snowballing*

  * [**4) Summarize a group of citations**](https://github.com/dvklopfenstein/pmidcite#4-summarize-a-group-of-citations)

  * [**5) Download citations for all papers returned from a PubMed search**](https://github.com/dvklopfenstein/pmidcite/blob/main/README.md#5-download-citations-for-all-papers-returned-from-a-pubmed-search)

* ***Examples in Jupyter notebooks using the *pmidcite* Python library***

  * [**1) Download NIH-OCC citation data**](https://github.com/dvklopfenstein/pmidcite/blob/main/notebooks/NIHOCC_data_download_always.ipynb)

  * [**2) Download missing or load existing NIH-OCC citation data**](https://github.com/dvklopfenstein/pmidcite/blob/main/notebooks/NIHOCC_data_download_or_import.ipynb)

  * [**3) Print a paper's citation and reference data**](https://github.com/dvklopfenstein/pmidcite/blob/main/notebooks/print_paper_all_refs_cites.ipynb)

  * [**4) Sort NIH iCite entries**](https://github.com/dvklopfenstein/pmidcite/blob/main/notebooks/print_paper_sort_cites.ipynb)

  * [**5) Query PubMed**](https://github.com/dvklopfenstein/pmidcite/blob/main/notebooks/query_pubmed.ipynb)

* ***Installation & citation***:

  * [**Installation**](#installation)

  * [**Setup**](#setup)

  * [**Google Scholar vs. PubMed**](https://github.com/dvklopfenstein/pmidcite/blob/main/README.md#pubmed-vs-google-scholar)

    * [**What is in PubMed?**](https://github.com/dvklopfenstein/pmidcite/blob/main/README.md#what-is-in-pubmed--take-a-quick-tour)

  * [**How to Cite *pmidcite***](#how-to-cite)

  * [**Contributing**](#contributing)

* [***References***](#references)

## 1) Download citation counts and data for a research paper

```$ icite -H 26032263```    

* This paper (PMID 26032263) has `25` citations, `10` references, and `4` authors.    

* This paper is performing well (`74`th percentile in column `%`) compared to its [peers](https://icite.od.nih.gov/user_guide?page_id=ug_overview).    

    

![Starting usage](https://github.com/dvklopfenstein/pmidcite/raw/main/docs/images/pmidcite0.png)

### NIH percentile

This paper is performing well (`74`th percentile) compared to its [peers](https://icite.od.nih.gov/user_guide?page_id=ug_overview) (column `%`).     

The NIH percentile grouping (column `G`) helps to

highlight the better performing papers in groups `2`, `3`, and `4` by

sorting the citing papers by group first, then publication year.

The sort places the lower performing papers in groups `0` or `1` at the back.

New papers appear at the beginning of a sorted list,

no matter how many citations they have to

better facilitate researchers in finding the latest discoveries.

The grouping of papers by NIH percentile grouping is a novel feature created by [dvklopfenstein](https://github.com/dvklopfenstein) for this project.

## 2) Forward citation search



Also known as following a paper's *Cited by* links or *Forward snowballing*    

```icite -H; icite 26032263 --load_citations | sort -k6 -r```    

or    

```icite -H; icite 26032263 -c | sort -k6 -r```    

## 3) Backward citation search

Also known as following links to a paper's references or *Backward snowballing*    



```$ icite -H; icite 26032263 --load_references | sort -k6 -r```    

or    

```$ icite -H; icite 26032263 -r | sort -k6 -r```     

## 4) Summarize a group of citations

Create a file containing numerous PMIDs annotated with icite info

```

$ icite 30022098 -c -o goatools_cites.txt

  WROTE: goatools_cites.txt

```

Count the number of lines in the file

```

$ wc -l goatools_cites.txt

468 goatools_cites.txt

```

Summarize the papers in "goatools_cites.txt"

```

$ sumpaps goatools_cites.txt

i=026.9% 4=003.0% 3=018.9% 2=028.8% 1=015.9% 0=006.5%   6 years:2018-2024   465 papers goatools_cites.txt

```

* The output is on one line so many files containing sets of PMIDs may be compared

* The groups are from newest(`i`) to top-performing(`4`), great(`3`), very good(`2`), and overlooked(`1` and `0`)

## 5) Download citations for all papers returned from a PubMed search

1. [Do a search in PubMed](#1-do-a-search-in-pubmed)

2. [Save all results into a file containing all PMIDs found by the search](#2-save-all-results-into-a-list-of-pmids)

3. [Download the list of PMIDs](#3-download-the-list-of-pmids)

4. [Run icite to analyze all the PMIDs](#4-run-icite-to-analyze-all-the-pmids)

### 1. Do a search in [PubMed](https://pubmed.ncbi.nlm.nih.gov/)

   

### 2. Save all results into a list of PMIDs

   

### 3. Download the list of PMIDs

   

### 4. Run icite to analyze all the PMIDs

```

$ icite -i pmid-HIVANDDNAm-set.txt -o pmid-HIVANDDNAm-icite.txt

$ grep TOP pmid-HIVANDDNAm-icite.txt | sort -k6

```

## Command Line Interface (CLI)

A Command-Line Interface (CLI) can be preferable 

to a Graphical User Interface (GUI) because: 

* processing can be automated from a script

* time-consuming mouse clicking is reduced

* more data can be seen at once on a text screen

than in a browser, giving the researcher 

a better overall impression of the full set of information [[1]](#how-to-cite)

Researchers who use Linux or Mac already work from the command line.

Researchers who use Windows can get that Linux-like command line feeling

while still running native Windows programs by

downloading Cygwin from https://www.cygwin.com/ [[1]](#how-to-cite).

# PubMed vs Google Scholar







In 2013, Boeker et al. [[6](#references)]

recommended that a scientific search interface contain five integrated search criteria. 

PubMed implements all five, while Google did not in 2013 or today.

Google's highly popular implementation of the forward citation search through their ubiquitous "Cited by N" links

is a "Better" experience than the PubMed's "forward citation search" implementation.

But if your research is in the health sciences and

you are amenable to working from the [command line](#command-line-interface-cli),

you can use PubMed in your browser plus

citation data downloaded from the NIH using the command-line  using *pmidcite*.

The NIH's citation data includes a paper's ranking among its co-citation network.

## What is in [PubMed](https://pubmed.ncbi.nlm.nih.gov)?  Take a [**quick tour**](https://www.nlm.nih.gov/pubs/techbull/ma20/brief/ma20_pubmed_essentials.html)



PubMed is a search interface and toolset used to access over 30.5 million article records from databases such as:

* **MEDLINE**: a highly selective database started in the 1960s

* **PubMed Central (PMC)**: an open-access database for full-text papers that are free of cost

* Additional content such as books and articles published before the 1960s

## Installation

To install from [**PyPI**](https://pypi.org/project/pmidcite/)    

```$ pip3 install pmidcite```

To install locally

```

$ git clone https://github.com/dvklopfenstein/pmidcite.git

$ cd ./pmidcite

$ pip3 install .

```

## Setup

Save your literature search in a GitHub repo.

### 1. Add a [pmidcite init file](doc/example_cfg/.pmidciterc)

Add a .pmidciterc init file to a non-git managed directory, such as home (~)

```

$ icite --generate-rcfile | tee ~/.pmidciterc

[pmidcite]

email = [email protected]

# To download PubMed search results, get an NCBI API key here:

# https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities

apikey = MY_LONG_HEX_NCBI_API_KEY

tool = my_scripts

```

```

$ export PMIDCITECONF=~/.pmidciterc

```

Do not version manage the `.pmidciterc` using a tool such as GitHub because it

contains your personal email and your private NCBI API key.

### 2. NCBI E-Utils API key

To download PubMed abstracts and PubMed search results using NCBI's E-Utils,

get an NCBI API key using these instructions:    

https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities

Set the `apikey` value in the config file: `~/.pmidciterc`

# Contributing

See the [**contributing guide**](/docs/CONTRIBUTING.md) for detailed instructions on how to get started contributing to the **pmidcite** project.

# Contact

email: [email protected]    

https://orcid.org/0000-0003-0161-7603

## How to Cite

_If you use **pmidcite** in your research or literature search, please cite paper 1 (pmidcite) and paper 3 (NIH citation data)._      

_Please also consider reading and citing Gusenbauer's response (paper 2) about improving search for all during the information avalanche of these times:_

1. **The *pmidcite* paper:**    

[**Commentary to Gusenbauer and Haddaway 2020: Evaluating Retrieval Qualities of PubMed and Google Scholar**](http://dx.doi.org/10.1002/jrsm.1456)    

Klopfenstein DV and Dampier W    

2020 | _Research Synthesis Methods_ | PMID: [33031632](https://pubmed.ncbi.nlm.nih.gov/33031632/) | DOI: [10.1002/jrsm.1456](http://dx.doi.org/10.1002/jrsm.1456) | [pdf](/doc/paper/JRSM_1456_iCite_main.pdf)

2. **Gusenbauer's response to the *pmidcite* paper:**    

[**What every Researcher should know about Searching – Clarified Concepts, Search Advice, and an Agenda to improve Finding in Academia**](https://onlinelibrary.wiley.com/doi/10.1002/jrsm.1457)    

Gusenbauer M and Haddaway N    

2020 | _Research Synthesis Methods_ | PMID: [33031639](https://pubmed.ncbi.nlm.nih.gov/33031639/) | DOI: [10.1002/jrsm.1457](https://onlinelibrary.wiley.com/doi/10.1002/jrsm.1457) | [pdf](/doc/paper/jrsm.1457.pdf)

3. **The NIH citation data used by *pmidcite* -- Scientific Influence, Translation, and Citation counts:**     

[**The NIH Open Citation Collection: A public access, broad coverage resource**](https://pubmed.ncbi.nlm.nih.gov/31600197/)    

Hutchins BI ... Santangelo GM    

2019 | _PLoS Biology_ | PMID: [31600197](https://pubmed.ncbi.nlm.nih.gov/31600197) | DOI: [10.1371/journal.pbio.3000385](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000385)    

## References

_Please consider reading and citing the paper [4] which inspired the creation of **pmidcite** [1] and the authors' response to our paper [2]_:

4. [**Which Academic Search Systems are Suitable for Systematic Reviews or Meta-Analyses? Evaluating Retrieval Qualities of Google Scholar, PubMed and 26 other Resources**](https://pubmed.ncbi.nlm.nih.gov/31614060/)    

Gusenbauer M and Haddaway N    

2019 | _Research Synthesis Methods_ | PMID: [31614060](https://pubmed.ncbi.nlm.nih.gov/31614060) | DOI: [10.1002/jrsm.1378](https://onlinelibrary.wiley.com/doi/full/10.1002/jrsm.1378)

_Mentioned in this README are also these outstanding contributions_:

5. [**Relative Citation Ratio (RCR): A New Metric That Uses Citation Rates to Measure Influence at the Article Level**](https://pubmed.ncbi.nlm.nih.gov/27599104/)    

Hutchins BI, Xin Yuan, Anderson JM, and Santangelo, George M.    

2016 | _PLoS Biology_ | PMID: [27599104](https://pubmed.ncbi.nlm.nih.gov/27599104) | DOI: [10.1371/journal.pbio.1002541](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002541)

6. [**Google Scholar as replacement for systematic literature searches: good relative recall and precision are not enough**](https://pubmed.ncbi.nlm.nih.gov/24160679/)    

Boeker M et al.    

2013 | BMC Medical Research Methodology | PMID: [24160679](https://pubmed.ncbi.nlm.nih.gov/24160679) | DOI: [10.1186/1471-2288-13-131](https://bmcmedresmethodol.biomedcentral.com/articles/10.1186/1471-2288-13-131)

7. [**Best Match: New relevance search for PubMed**](https://pubmed.ncbi.nlm.nih.gov/30153250/)    

Fiorini N ... Lu Zhiyong    

2018 | PLoS Biology | PMID: [30153250](https://pubmed.ncbi.nlm.nih.gov/30153250) | DOI: [10.1371/journal.pbio.2005343](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2005343)    

## [PDFs](/doc/paper/JRSM_1456_iCite_main.pdf)

  * [**PMIDCITE Manuscript**](/doc/paper/JRSM_1456_iCite_main.pdf) with the original text box formatting

    * **Supplemental Material**

      * [S1. *pmidcite* information](/doc/paper/JRSM_1456_iCite_supp1_CitedByN.pdf)

      * [S2. Contents of PubMed](/doc/paper/JRSM_1456_iCite_supp2_PMcontents.pdf)

      * [S3. Screen shots Google Scholar taken Jan 2020](/doc/paper/JRSM_1456_iCite_supp3_GS.pdf)

  * [**Gusenbauer's Response**](/doc/paper/jrsm.1457.pdf)

## Contact

[email protected]    

https://orcid.org/0000-0003-0161-7603

Copyright (C) 2019-present [pmidcite](https://dvklopfenstein.github.io/pmidcite/), DV Klopfenstein, PhD. All rights reserved.