Package: pmidcite
PubMed ID (PMID) CiteTurbocharge aPubMedliterature search in biomedicine, biochemistry, chemistry, behavioral science, and other life sciences by linkingcitation datafrom theNational Institutes of Health (NIH)withPubMedIDs (PMIDs) using the command line rather than clicking and clicking and clicking onGoogle Scholar"Cited by N" links.This open-source project is part ofa peer-reviewedcommentarythat was invited by the editors ofResearch Synthesis Methods.
PleaseCiteif you usepmidcitein your research or literature search.Contact:dvklopfenstein@protonmail.comTable of ContentsQuickstart on thecommand line1) Download citation counts and data for a research paper2) Forward citation search: following a paper'sCited bylinks orForward snowballing3) Backward citation search: following the links to a paper's references orBackward snowballing4) Summarize a group of citations5) Search PubMed from the command lineExamples in Jupyter notebooks using thepmidcitePython library1) Download NIH-OCC citation data2) Download missing or load existing NIH-OCC citation data3) Print a paper's citation and reference data4) Sort NIH iCite entries5) Query PubMedInstallation & citation:InstallationSetupGoogle Scholar vs. PubMedWhat is in PubMed?How to CitepmidciteContributingReferences1) Download citation counts and data for a research paper$ icite -H 26032263This paper (PMID 26032263) has25citations,10references, and4authors.This paper is performing well (74th percentile in column%) compared to itspeers.NIH percentileThis paper is performing well (74th percentile) compared to itspeers(column%).The NIH percentile grouping (columnG) helps to
highlight the better performing papers in groups2,3, and4by
sorting the citing papers by group first, then publication year.The sort places the lower performing papers in groups0or1at 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 bydvklopfensteinfor this project.2) Forward citation searchAlso known as following a paper'sCited bylinks orForward snowballingicite -H; icite 26032263 --load_citations | sort -k6 -roricite -H; icite 26032263 -c | sort -k6 -r3) Backward citation searchAlso known as following links to a paper's references orBackward snowballing$ icite -H; icite 26032263 --load_references | sort -k6 -ror$ icite -H; icite 26032263 -r | sort -k6 -r4) Summarize a group of citations4a) Examine a paper with PMID30022098. Print the column headers(-H):icite -H 300220984b) Download the details about each paper(-c) that cites30022098into a file(-o goatools_cites.txt):icite 30022098 -c -o goatools_cites.txt4c) Summarize the overall performace of the 300+ citing papers contained ingoatools_cites.txtsummarize_papers goatools_cites.txt -p TOP CIT CLI4a) Examine a paper with PMID30022098. Print the column headers(-H):$ icite -H 30022098
COL 2        3  4       5 6 7        8  9  10 au[11](authors)
TYP PMID     RP HAMCc   % G YEAR   cit cli ref au[00](authors) title
TOP 30022098 R. .A..c 100 4 2018   318  1  23 au[14](D V Klopfenstein) GOATOOLS: A Python library for Gene Ontology analyses.Paper with PMID30022098is cited by318(cit) other research papers and1(cli) clinical study. It has23references(ref).4b) Download the details about each paper(-c) that cites30022098into a file(-o goatools_cites.txt):$ icite 30022098 -c -o goatools_cites.txtThe requested paper (PMID=30022098) is described in one one line ingoatools_cites.txt:$ grep TOP goatools_cites.txt
TOP 30022098 R. .A..c 100 4 2018   318  1  23 au[14](D V Klopfenstein) GOATOOLS: A Python library for Gene Ontology analyses.The paper (PMID=30022098) is cited by 381(CIT) research papers plus 1(CLI) clinical study:$ grep CIT goatools_cites.txt | wc -l
318

$ grep CLI goatools_cites.txt | wc -l
14c) Summarize all the papers ingoatools_cites.txtNEW FUNCTIONALITY; INPUT REQUESTED: What would you like to see?Open an issueto comment.$ summarize_papers goatools_cites.txt -p TOP CIT CLI
i=033.4% 4=003.4% 3=020.9% 2=021.9% 1=015.9% 0=004.4%   4 years:2018-2022   320 papers goatools_cites.txtOutput is on one line so many files containing sets of PMIDs may be compared. TBD: Add multiline verbose option.The groups are from newest(i) to top-performing(4), great(3), very good(2), and overlooked(1and0)The percentages of papers ingoatools_citations.txtin each group follow the group name5) Download citations for all papers returned from a PubMed searchDo a search in PubMedSave all results into a file containing all PMIDs found by the searchDownload the list of PMIDsRun icite to analyze all the PMIDs1. Do a search inPubMed2. Save all results into a list of PMIDs3. Download the list of PMIDs4. 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 -k6Command Line Interface (CLI)A Command-Line Interface (CLI) can be preferable
to a Graphical User Interface (GUI) because:processing can be automated from a scripttime-consuming mouse clicking is reducedmore 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]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 fromhttps://www.cygwin.com/[1].PubMed vs Google ScholarIn 2013, Boeker et al. [6]
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 thecommand line,
you can use PubMed in your browser plus
citation data downloaded from the NIH using the command-line  usingpmidcite.
The NIH's citation data includes a paper's ranking among its co-citation network.What is inPubMed?  Take aquick tourPubMed 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 1960sPubMed Central (PMC): an open-access database for full-text papers that are free of costAdditional content such as books and articles published before the 1960sInstallationTo install fromPyPI$ pip3 install pmidciteTo install locally$ git clone https://github.com/dvklopfenstein/pmidcite.git
$ cd ./pmidcite
$ pip3 install .SetupSave your literature search in a GitHub repo.1. Add apmidcite init fileAdd a .pmidciterc init file to a non-git managed directory, such as home (~)$ icite --generate-rcfile | tee ~/.pmidciterc
[pmidcite]
email = myname@email.edu
# 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=~/.pmidcitercDo not version manage the.pmidcitercusing a tool such as GitHub because it
contains your personal email and your private NCBI API key.2. NCBI E-Utils API keyTo 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-utilitiesSet theapikeyvalue in the config file:~/.pmidcitercContributingSee thecontributing guidefor detailed instructions on how to get started contributing to thepmidciteproject.Contactemail:dvklopfenstein@protonmail.comhttps://orcid.org/0000-0003-0161-7603How to CiteIf you usepmidcitein 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:Thepmidcitepaper:Commentary to Gusenbauer and Haddaway 2020: Evaluating Retrieval Qualities of PubMed and Google ScholarKlopfenstein DV and Dampier W2020 |Research Synthesis Methods| PMID:33031632| DOI:10.1002/jrsm.1456|pdfGusenbauer's response to thepmidcitepaper:What every Researcher should know about Searching – Clarified Concepts, Search Advice, and an Agenda to improve Finding in AcademiaGusenbauer M and Haddaway N2020 |Research Synthesis Methods| PMID:33031639| DOI:10.1002/jrsm.1457|pdfThe NIH citation data used bypmidcite-- Scientific Influence, Translation, and Citation counts:The NIH Open Citation Collection: A public access, broad coverage resourceHutchins BI ... Santangelo GM2019 |PLoS Biology| PMID:31600197| DOI:10.1371/journal.pbio.3000385ReferencesPlease consider reading and citing the paper [4] which inspired the creation ofpmidcite[1] and the authors' response to our paper [2]:Which Academic Search Systems are Suitable for Systematic Reviews or Meta-Analyses? Evaluating Retrieval Qualities of Google Scholar, PubMed and 26 other ResourcesGusenbauer M and Haddaway N2019 |Research Synthesis Methods| PMID:31614060| DOI:10.1002/jrsm.1378Mentioned in this README are also these outstanding contributions:Relative Citation Ratio (RCR): A New Metric That Uses Citation Rates to Measure Influence at the Article LevelHutchins BI, Xin Yuan, Anderson JM, and Santangelo, George M.2016 |PLoS Biology| PMID:27599104| DOI:10.1371/journal.pbio.1002541Google Scholar as replacement for systematic literature searches: good relative recall and precision are not enoughBoeker M et al.2013 | BMC Medical Research Methodology | PMID:24160679| DOI:10.1186/1471-2288-13-131Best Match: New relevance search for PubMedFiorini N ... Lu Zhiyong2018 | PLoS Biology | PMID:30153250| DOI:10.1371/journal.pbio.2005343PDFsPMIDCITE Manuscriptwith the original text box formattingSupplemental MaterialS1.pmidciteinformationS2. Contents of PubMedS3. Screen shots Google Scholar taken Jan 2020Gusenbauer's ResponseContactdvklopfenstein@protonmail.comhttps://orcid.org/0000-0003-0161-7603Copyright (C) 2019-presentpmidcite, DV Klopfenstein, PhD. All rights reserved.