pubmedR is an R package for gathering bibliographic metadata from the PubMed database using NCBI Entrez REST APIs.
It provides a complete toolkit to search, download, convert, and enrich PubMed records, with full compatibility with the bibliometrix R package for bibliometric analysis.
| Function | Description |
|---|---|
pmQueryBuild() |
Build a PubMed query programmatically |
pmQueryTotalCount() |
Count the number of records matching a query |
pmApiRequest() |
Download bibliographic metadata from PubMed |
pmApi2df() |
Convert downloaded XML data into a data frame |
pmFetchById() |
Download records by a list of PMIDs |
pmCitedBy() |
Find articles that cite a given article |
pmReferences() |
Find references cited by a given article |
pmEnrichCitations() |
Add citation counts and references to a data frame |
pmCollect() |
One-step wrapper for the full workflow |
You can install the released version of pubmedR from CRAN with:
install.packages("pubmedR")Or install the development version from GitHub:
# install.packages("devtools")
devtools::install_github("massimoaria/pubmedR")Access to the NCBI PubMed API is free and does not necessarily require an API key. However, without a key, NCBI limits requests to 3 per second. With a registered API key, the limit increases to 10 per second.
To obtain a free API key:
- Register for a My NCBI account
- Go to your Account Settings and generate an API key
You can set the API key in three ways (in order of priority):
# Option 1: Pass it directly to functions
D <- pmApiRequest(query = query, limit = 100, api_key = "your_api_key")
# Option 2: Set the PUBMED_API_KEY environment variable in your .Renviron
# Run: usethis::edit_r_environ()
# Then add: PUBMED_API_KEY=your_api_key
# Option 3: Use the ENTREZ_KEY variable (rentrez convention)
# ENTREZ_KEY=your_api_keyWhen the API key is set via environment variable, all pubmedR functions will use it automatically.
library(pubmedR)The fastest way to get PubMed data into R is pmCollect(), which
handles the entire workflow in a single call:
# Collect bibliometric articles published between 2020 and 2024
M <- pmCollect(
terms = "bibliometric*",
language = "english",
pub_type = "Journal Article",
date_range = c("2020", "2024"),
limit = 10
)M[, c("AU", "PY", "TI", "SO")]
#> AU
#> 1 LLONTO CAICEDO Y;MORÁN SANTAMARÍA RO;ALARCÓN VILLANUEVA G;ZAVALETA GONZÁLES LN;LLATAS DÍAZ WD;PACHECO GONZALES IB;PEJERREY GONZÁLEZ RJ;CASTRO MEJÍA PJ;ATALAYA URRUTIA CW
#> 2 SALEH AY;VALENTINA R;SUSANTO TD;SAPUTRA DAY
#> 3 VELASQUEZ GARCIA A;MINAMI M;MEJIA-RODRÍGUEZ M;ORTÍZ-MORALES JR;RADICE F
#> 4 MUNAGA S;ALSHEHRI A;UL-HAQ I;KALAGI S;CHITUMALLA R;IYER K
#> 5 VALENCIA-ARIAS A;CARDONA-ACEVEDO S;MARTÍNEZ ROJAS E;RAMÍREZ DÁVILA J;RODRIGUEZ-CORREA P;PALACIOS-MOYA L;TEODORI DE LA PUENTE R;AGUDELO-CEBALLOS E;BENJUMEA-ARIAS M
#> 6 JIANG F;LI X;QIAO Q;ZHANG G;ZHANG Y;SU L
#> 7 DYESS GA;GHALIB MA;TAYLOR Z;SABETTA Z;TAYLOR E;BUTLER D;BASSETT M;HARRIS L;BOLUS H;SHAHID A;THAKUR JD
#> 8 NAVARRETE CB;CASTILLO LV;QUIÑONES AS;RODRÍGUEZ IR;MORENO LS
#> 9 MARTINHO VJPD;BRÓZDOWSKI J
#> 10 PHANG KC;NG TC;SINGH SKG;VOO TC;ALVIS WA
#> PY
#> 1 2025
#> 2 2025
#> 3 2024
#> 4 2024
#> 5 2025
#> 6 2024
#> 7 2024
#> 8 2024
#> 9 2025
#> 10 2024
#> TI
#> 1 URBAN PLANNING EFFECTIVENESS AND CITIZEN SATISFACTION. A SYSTEMATIC LITERATURE REVIEW.
#> 2 BEYOND STROKE THERAPY, NEUROAID (A CHINESE HERBAL) HAS AN EFFECT ON COGNITION AND NEUROGENESIS, A BIBLIOMETRIC STUDY.
#> 3 LARGE LANGUAGE MODELS IN ORTHOPEDICS: AN EXPLORATORY RESEARCH TREND ANALYSIS AND MACHINE LEARNING CLASSIFICATION.
#> 4 SAUDI ARABIA'S CONTRIBUTION TO SYSTEMATIC REVIEWS IN DENTISTRY: A BIBLIOMETRIC ANALYSIS.
#> 5 TRENDS IN SMART RESTAURANT RESEARCH: BIBLIOMETRIC REVIEW AND RESEARCH AGENDA.
#> 6 KNOWLEDGE MAPPING OF ASPERGILLUS-RELATED RESEARCH IN RESPIRATORY MEDICINE: A BIBLIOMETRIC ANALYSIS BASED ON ENGLISH-LANGUAGE ARTICLES SPANNING 1975 TO 2022.
#> 7 CAREERS IN SKULL BASE AND OPEN CEREBROVASCULAR SURGERY: FACTORS ASSOCIATED WITH ACADEMIC JOB PLACEMENT.
#> 8 INTERNATIONALIZATION AND COLLABORATION IN COLOMBIAN PSYCHOLOGY DURING 2014-2023: A BIBLIOMETRIC ANALYSIS.
#> 9 SUGGESTIONS FOR RESIN RESEARCH UNDER THE COST ACTION EU-POTARCH.
#> 10 NAVIGATING ARTIFICIAL INTELLIGENCE IN MALAYSIAN HEALTHCARE: RESEARCH DEVELOPMENTS, ETHICAL DILEMMAS, AND GOVERNANCE STRATEGIES.
#> SO
#> 1 F1000RESEARCH
#> 2 F1000RESEARCH
#> 3 JOURNAL OF ORTHOPAEDICS
#> 4 THE SAUDI DENTAL JOURNAL
#> 5 F1000RESEARCH
#> 6 CANADIAN RESPIRATORY JOURNAL
#> 7 JOURNAL OF NEUROLOGICAL SURGERY. PART B, SKULL BASE
#> 8 PSYCHOLOGY IN RUSSIA : STATE OF THE ART
#> 9 OPEN RESEARCH EUROPE
#> 10 ASIAN BIOETHICS REVIEWYou can also pass a raw query string and enable citation enrichment:
M_enriched <- pmCollect(
query = "bibliometric*[Title/Abstract] AND english[LA] AND 2023:2024[DP]",
limit = 5,
enrich = TRUE
)M_enriched[, c("AU", "PY", "TC")]
#> AU
#> 1 LLONTO CAICEDO Y;MORÁN SANTAMARÍA RO;ALARCÓN VILLANUEVA G;ZAVALETA GONZÁLES LN;LLATAS DÍAZ WD;PACHECO GONZALES IB;PEJERREY GONZÁLEZ RJ;CASTRO MEJÍA PJ;ATALAYA URRUTIA CW
#> 2 SALEH AY;VALENTINA R;SUSANTO TD;SAPUTRA DAY
#> 3 VELASQUEZ GARCIA A;MINAMI M;MEJIA-RODRÍGUEZ M;ORTÍZ-MORALES JR;RADICE F
#> 4 MUNAGA S;ALSHEHRI A;UL-HAQ I;KALAGI S;CHITUMALLA R;IYER K
#> 5 VALENCIA-ARIAS A;CARDONA-ACEVEDO S;MARTÍNEZ ROJAS E;RAMÍREZ DÁVILA J;RODRIGUEZ-CORREA P;PALACIOS-MOYA L;TEODORI DE LA PUENTE R;AGUDELO-CEBALLOS E;BENJUMEA-ARIAS M
#> PY TC
#> 1 2025 0
#> 2 2025 0
#> 3 2024 1
#> 4 2024 0
#> 5 2025 0For more control over each step, you can use the individual functions described below.
The pmQueryBuild() function helps you construct valid PubMed queries
programmatically:
# Build a query for bibliometric articles in English, published between 2015 and 2024
query <- pmQueryBuild(
terms = "bibliometric*",
fields = "Title/Abstract",
language = "english",
pub_type = "Journal Article",
date_range = c("2015", "2024")
)
query
#> [1] "bibliometric*[Title/Abstract] AND english[LA] AND Journal Article[PT] AND 2015:2024[DP]"You can also combine multiple terms and add MeSH filters:
# Combine multiple terms with OR
query_ml <- pmQueryBuild(
terms = c("machine learning", "deep learning", "artificial intelligence"),
fields = "Title/Abstract",
operator = "OR",
mesh_terms = "Neoplasms",
language = "english",
date_range = c("2020", "2024")
)
query_ml
#> [1] "(machine learning[Title/Abstract] OR deep learning[Title/Abstract] OR artificial intelligence[Title/Abstract]) AND Neoplasms[MeSH Terms] AND english[LA] AND 2020:2024[DP]"Of course, you can also write the query string manually using the Entrez query syntax:
query <- "bibliometric*[Title/Abstract] AND english[LA] AND Journal Article[PT] AND 2015:2024[DP]"Before downloading, check how many records match your query:
res <- pmQueryTotalCount(query = query)
res$total_count
#> [1] 12451
res$query_translation
#> [1] "\"bibliometric*\"[Title/Abstract] AND \"english\"[Language] AND \"journal article\"[Publication Type] AND 2015/01/01:2024/12/31[Date - Publication]"Download metadata for the matching records:
D <- pmApiRequest(query = query, limit = 200)The pmApiRequest() function returns a list with five elements:
- data: XML-structured list of bibliographic metadata
- query: the original query
- query_translation: query translated by NCBI
- records_downloaded: number of records downloaded
- total_count: total number of matching records
Convert the downloaded XML data into a structured data frame:
M <- pmApi2df(D, format = "bibliometrix")dplyr::glimpse(M)
#> Rows: 200
#> Columns: 31
#> $ AU <chr> "LLONTO CAICEDO Y;MORÁN SANTAMARÍA RO;ALARCÓN VILLANUEVA G;Z…
#> $ AF <chr> "LLONTO CAICEDO, YEFFERSON;MORÁN SANTAMARÍA, ROGGER ORLANDO;…
#> $ TI <chr> "URBAN PLANNING EFFECTIVENESS AND CITIZEN SATISFACTION. A SY…
#> $ SO <chr> "F1000RESEARCH", "F1000RESEARCH", "JOURNAL OF ORTHOPAEDICS",…
#> $ SO_CO <chr> "ENGLAND", "ENGLAND", "INDIA", "SAUDI ARABIA", "ENGLAND", "U…
#> $ LA <chr> "ENG", "ENG", "ENG", "ENG", "ENG", "ENG", "ENG", "ENG", "ENG…
#> $ DT <chr> "JOURNAL ARTICLE", "JOURNAL ARTICLE", "JOURNAL ARTICLE", "JO…
#> $ DE <chr> "PRISMA;BIBLIOMETRICS;BIBLIOMETRIX;CITIZEN SATISFACTION;STAT…
#> $ ID <chr> "CITY PLANNING;HUMANS;PERSONAL SATISFACTION;QUALITY OF LIFE;…
#> $ MESH <chr> "CITY PLANNING;HUMANS;PERSONAL SATISFACTION;QUALITY OF LIFE;…
#> $ AB <chr> "THE POPULATION IS INCREASINGLY DEMANDING A BETTER QUALITY O…
#> $ C1 <chr> "LAMBAYEQUE, UNIVERSIDAD NACIONAL PEDRO RUIZ GALLO, LAMBAYEQ…
#> $ CR <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
#> $ TC <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
#> $ SN <chr> "2046-1402", "2046-1402", "0972-978X", "1013-9052", "2046-14…
#> $ J9 <chr> "F1000RES", "F1000RES", "J ORTHOP", "SAUDI DENT J", "F1000RE…
#> $ JI <chr> "F1000RES", "F1000RES", "J ORTHOP", "SAUDI DENT J", "F1000RE…
#> $ PY <dbl> 2025, 2025, 2024, 2024, 2025, 2024, 2024, 2024, 2025, 2024, …
#> $ PY_IS <chr> "2024", "2024", "2025", "2024", "2024", "2024", "2025", "202…
#> $ VL <chr> "13", "13", "66", "36", "13", "2024", "86", "17", "4", "17",…
#> $ IS <chr> NA, NA, NA, "12", NA, NA, "5", "4", NA, "3", "1", "4", NA, N…
#> $ DI <chr> "10.12688/f1000research.157550.2", "10.12688/f1000research.1…
#> $ PG <chr> "1330", "799", "110-118", "1521-1526", "1505", "6199860", "5…
#> $ GRANT_ID <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
#> $ GRANT_ORG <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
#> $ UT <chr> "41287786", "41024939", "40978518", "40952837", "40919447", …
#> $ PMID <chr> "41287786", "41024939", "40978518", "40952837", "40919447", …
#> $ DB <chr> "PUBMED", "PUBMED", "PUBMED", "PUBMED", "PUBMED", "PUBMED", …
#> $ AU_UN <chr> "LAMBAYEQUE, UNIVERSIDAD NACIONAL PEDRO RUIZ GALLO, LAMBAYEQ…
#> $ AU_CO <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
#> $ AU1_CO <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …The format = "bibliometrix" option (default) creates a data frame
fully compatible with the bibliometrix
package, using standard bibliometric field tags:
| Tag | Description |
|---|---|
| AU | Authors |
| TI | Title |
| SO | Source (Journal) |
| AB | Abstract |
| DE | Author Keywords |
| ID | MeSH Terms |
| DI | DOI |
| PY | Publication Year |
| C1 | Author Affiliations |
| TC | Times Cited |
| CR | Cited References |
| … | and more |
If you already have a list of PubMed IDs, use pmFetchById() to
download their metadata directly:
pmids <- c("25824007", "28981534", "31414462")
D_pmid <- pmFetchById(pmids = pmids)M_pmid <- pmApi2df(D_pmid)M_pmid[, c("AU", "PY", "TI", "SO")]
#> AU
#> 1 CASTER DJ;KORTE EA;MERCHANT ML;KLEIN JB;WILKEY DW;ROVIN BH;BIRMINGHAM DJ;HARLEY JB;COBB BL;NAMJOU B;MCLEISH KR;POWELL DW
#> 2 GLÜGE J;STEINLIN C;SCHALLES S;WEGMANN L;TREMP J;BREIVIK K;HUNGERBÜHLER K;BOGDAL C
#> 3 EO
#> PY
#> 1 2014
#> 2 2017
#> 3 2019
#> TI
#> 1 AUTOANTIBODIES TARGETING GLOMERULAR ANNEXIN A2 IDENTIFY PATIENTS WITH PROLIFERATIVE LUPUS NEPHRITIS.
#> 2 IMPORT, USE, AND EMISSIONS OF PCBS IN SWITZERLAND FROM 1930 TO 2100.
#> 3 [NOT AVAILABLE].
#> SO
#> 1 PROTEOMICS. CLINICAL APPLICATIONS
#> 2 PLOS ONE
#> 3 MMW FORTSCHRITTE DER MEDIZINPubMed does not provide citation counts or reference lists by default. pubmedR can enrich your data using the NCBI E-Link service.
# Find who cited a specific article (PMID: 25824007)
cites <- pmCitedBy(pmid = "25824007")
cat("Number of citing articles:", cites$count, "\n")
#> Number of citing articles: 31
cat("First 5 citing PMIDs:", paste(head(cites$cited_by, 5), collapse = ", "), "\n")
#> First 5 citing PMIDs: 41021815, 40889685, 39057791, 38891801, 37955107# Find the references of an article
refs <- pmReferences(pmid = "25824007")
cat("Number of references:", refs$count, "\n")
#> Number of references: 62
cat("First 5 reference PMIDs:", paste(head(refs$references, 5), collapse = ", "), "\n")
#> First 5 reference PMIDs: 25533130, 25273097, 25248362, 24845390, 24790181Use pmEnrichCitations() to add citation data (TC and CR fields) to an
entire data frame:
# Enrich the small PMID dataset with citation data
M_enriched <- pmEnrichCitations(M_pmid)M_enriched[, c("AU", "PY", "TC", "CR")]
#> AU
#> 1 CASTER DJ;KORTE EA;MERCHANT ML;KLEIN JB;WILKEY DW;ROVIN BH;BIRMINGHAM DJ;HARLEY JB;COBB BL;NAMJOU B;MCLEISH KR;POWELL DW
#> 2 GLÜGE J;STEINLIN C;SCHALLES S;WEGMANN L;TREMP J;BREIVIK K;HUNGERBÜHLER K;BOGDAL C
#> 3 EO
#> PY TC
#> 1 2014 31
#> 2 2017 2
#> 3 2019 0
#> CR
#> 1 TSOKOS GC, 2011, N ENGL J MED, V365, P2110, DOI 10.1056/NEJMRA1100359; COZZANI E, 2013, AUTOIMMUNE DIS, V2014, P321359, DOI 10.1155/2014/321359; BHINDER S, 2010, AM J MED SCI, V339, P230, DOI 10.1097/MAJ.0B013E3181C9529C; WEENING JJ, 2004, KIDNEY INT, V65, P521, DOI 10.1111/J.1523-1755.2004.00443.X; MANNIK M, 2003, J RHEUMATOL, V30, P1495; SERET G, 2011, CLIN DEV IMMUNOL, V2012, P579670, DOI 10.1155/2012/579670; HANROTEL-SALIOU C, 2010, CLIN REV ALLERGY IMMUNOL, V40, P151, DOI 10.1007/S12016-010-8204-4; OLSON SW, 2013, CLIN J AM SOC NEPHROL, V8, P1702, DOI 10.2215/CJN.01910213; KALAAJI M, 2006, AM J PATHOL, V168, P1779, DOI 10.2353/AJPATH.2006.051329; BIRMINGHAM DJ, 2012, LUPUS, V21, P855, DOI 10.1177/0961203312439640; RASMUSSEN A, 2010, RHEUMATOLOGY (OXFORD), V50, P47, DOI 10.1093/RHEUMATOLOGY/KEQ302; YAMAMOTO T. RENAL AND URINARY PROTEOMICS. WILEY-VCH VERLAG GMBH & CO. KGAA; 2009. PP. 1–7.; SALEEM MA, 2002, J AM SOC NEPHROL, V13, P630, DOI 10.1681/ASN.V133630; BECK LH, 2009, N ENGL J MED, V361, P11, DOI 10.1056/NEJMOA0810457; POWELL DW, 2003, MOL CELL BIOL, V23, P5376, DOI 10.1128/MCB.23.15.5376-5387.2003; CUMMINS TD, 2009, BIOCHIM BIOPHYS ACTA, V1804, P653, DOI 10.1016/J.BBAPAP.2009.09.029; BABA SP, 2013, J BIOL CHEM, V288, P28163, DOI 10.1074/JBC.M113.504753; KELLER A, 2002, ANAL CHEM, V74, P5383, DOI 10.1021/AC025747H; NESVIZHSKII AI, 2003, ANAL CHEM, V75, P4646, DOI 10.1021/AC0341261; ASHBURNER M, 2000, NAT GENET, V25, P25, DOI 10.1038/75556; SEILER CY, 2013, NUCLEIC ACIDS RES, V42, PD1253, DOI 10.1093/NAR/GKT1060; DELVILLE M, 2014, SCI TRANSL MED, V6, P256RA136, DOI 10.1126/SCITRANSLMED.3008538; LEFRANC D, 2007, ARTHRITIS RHEUM, V56, P3420, DOI 10.1002/ART.22863; REISER J, 2000, J AM SOC NEPHROL, V11, P1, DOI 10.1681/ASN.V1111; PERYSINAKI GS, 2011, LUPUS, V20, P781, DOI 10.1177/0961203310397412; WELSH GI, 2011, NAT REV NEPHROL, V8, P14, DOI 10.1038/NRNEPH.2011.151; GREKA A, 2012, SEMIN NEPHROL, V32, P319, DOI 10.1016/J.SEMNEPHROL.2012.06.003; GEE HY, 2013, J CLIN INVEST, V123, P3243, DOI 10.1172/JCI69134; MEYER-SCHWESINGER C, 2012, AM J PHYSIOL RENAL PHYSIOL, V303, PF1015, DOI 10.1152/AJPRENAL.00380.2011; BHARADWAJ A, 2013, INT J MOL SCI, V14, P6259, DOI 10.3390/IJMS14036259; YUNG S, 2010, J AM SOC NEPHROL, V21, P1912, DOI 10.1681/ASN.2009080805; PIERCHALA BA, 2010, KIDNEY INT, V78, P868, DOI 10.1038/KI.2010.212; MARKOFF A, 2005, AM J PHYSIOL RENAL PHYSIOL, V289, PF949, DOI 10.1152/AJPRENAL.00089.2005; RESCHER U, 2008, J CELL SCI, V121, P2177, DOI 10.1242/JCS.028415; CAÑAS F, 2014, THROMB RES, V135, P226, DOI 10.1016/J.THROMRES.2014.11.034; MARTIN M, 2012, J BIOL CHEM, V287, P33733, DOI 10.1074/JBC.M112.341339; LEFFLER J, 2014, ANN RHEUM DIS, V73, P1601, DOI 10.1136/ANNRHEUMDIS-2014-205287; DÍAZ-RAMOS A, 2012, J BIOMED BIOTECHNOL, V2012, P156795, DOI 10.1155/2012/156795; BRUSCHI M, 2014, J AM SOC NEPHROL, V25, P2483, DOI 10.1681/ASN.2013090987; BRUSCHI M, 2011, J PROTEOMICS, V74, P2008, DOI 10.1016/J.JPROT.2011.05.021; HSU HH, 2007, J MOL MED (BERL), V86, P1379, DOI 10.1007/S00109-008-0399-Y; HUGO C, 1996, J CLIN INVEST, V97, P2499, DOI 10.1172/JCI118697; SUZUKI K, 2013, NEPHROL DIAL TRANSPLANT, V29, P1168, DOI 10.1093/NDT/GFT469; DOYLE A, 2011, J STRUCT BIOL, V176, P370, DOI 10.1016/J.JSB.2011.09.004; WIEGE K, 2012, J IMMUNOL, V189, P980, DOI 10.4049/JIMMUNOL.1200891; ZHOU CJ, 2003, EXP EYE RES, V77, P423, DOI 10.1016/S0014-4835(03)00171-4; ZANIN-ZHOROV A, 2003, FASEB J, V17, P1567, DOI 10.1096/FJ.02-1139FJE; LANG A, 2004, J AM SOC NEPHROL, V16, P383, DOI 10.1681/ASN.2004040276; HURST IR, 2003, J BONE MINER RES, V19, P499, DOI 10.1359/JBMR.0301238; AKIYAMA K, 2007, MAMM GENOME, V19, P41, DOI 10.1007/S00335-007-9078-5; LU Y, 2011, MOL CELL PROTEOMICS, V11, PM111.008755, DOI 10.1074/MCP.M111.008755; LIN CP, 2011, GENES IMMUN, V13, P232, DOI 10.1038/GENE.2011.82; CHEN HH, 2012, MOL CELL BIOL, V32, P2224, DOI 10.1128/MCB.06550-11; KREMER BE, 2006, CELL, V130, P837, DOI 10.1016/J.CELL.2007.06.053; ROSENTRETER A, 2006, EXP CELL RES, V313, P878, DOI 10.1016/J.YEXCR.2006.12.015; LIANG P, 1997, J CELL SCI, V110 ( PT 13), P1431, DOI 10.1242/JCS.110.13.1431; KHUNKEAWLA P, 2001, IMMUNOBIOLOGY, V203, P659, DOI 10.1016/S0171-2985(01)80015-2; KOSUGI T, 2014, NEPHROL DIAL TRANSPLANT, V30, P1097, DOI 10.1093/NDT/GFU302; WASIK AA, 2013, AM J PATHOL, V184, P1727, DOI 10.1016/J.AJPATH.2014.03.002; OSTALSKA-NOWICKA D, 2006, J CLIN PATHOL, V59, P916, DOI 10.1136/JCP.2005.031732; AHN YH, 2012, J CLIN INVEST, V122, P3170, DOI 10.1172/JCI63608; SCHMIEDER S, 2004, J AM SOC NEPHROL, V15, P2289, DOI 10.1097/01.ASN.0000135968.49899.E8; ZHA D, 2013, BMB REP, V46, P230, DOI 10.5483/BMBREP.2013.46.4.270
#> 2 HALSE AK, SCHLABACH M, ECKHARDT S, SWEETMAN AJ, JONES KC, BREIVIK K. SPATIAL VARIABILITY OF POPS IN EUROPEAN BACKGROUND AIR. ATMOS CHEM PHYS. 2011;11(4):1549–1564. 10.5194/ACP-11-1549-2011; BOGDAL C, 2010, ENVIRON SCI TECHNOL, V44, P4063, DOI 10.1021/ES903007H; LI YF, 2010, ENVIRON SCI TECHNOL, V44, P2784, DOI 10.1021/ES901871E; JEPSON PD, 2015, SCI REP, V6, P18573, DOI 10.1038/SREP18573; WÖHRNSCHIMMEL H, 2015, ENVIRON POLLUT, V217, P149, DOI 10.1016/J.ENVPOL.2016.01.090; JEPSON PD, 2016, SCIENCE, V352, P1388, DOI 10.1126/SCIENCE.AAF9075; LRTAP. CONVENTION ON LONG-RANGE TRANSBOUNDARY AIR POLLUTION; 1979. AVAILABLE FROM: HTTPS://WWW.UNECE.ORG/FILEADMIN/DAM/ENV/LRTAP/FULLTEXT/1979.CLRTAP.E.PDF; UNECE. PROTOCOL TO THE 1979 CONVENTION ON LONG-RANGE TRANSBOUNDARY AIR POLLUTION ON PERSISTENT ORGANIC POLLUTANTS. UNITED NATIONS ECONOMIC COMMISSION FOR EUROPE (UNECE); 1998. AVAILABLE FROM: HTTP://WWW.UNECE.ORG/FILEADMIN/DAM/ENV/LRTAP/FULLTEXT/1998.POPS.E.PDF; UNECE. GUIDELINES FOR REPORTING EMISSIONS AND PROJECTIONS DATA UNDER THE CONVENTION ON LONG-RANGE TRANSBOUNDARY AIR POLLUTION (ECE/EB-AIR/97). UNITED NATIONS ECONOMIC COMMISSION FOR EUROPE (UNECE); 2009. AVAILABLE FROM: HTTPS://WWW.UNECE.ORG/FILEADMIN/DAM/ENV/DOCUMENTS/2012/AIR/GUIDELINES_FOR_REPORTING_EMISSION_DATA_UNDER_THE_CLRTAP.PDF; EEA. EMEP/EEA AIR POLLUTANT EMISSION INVENTORY GUIDEBOOK 2016. TECHNICAL GUIDANCE TO PREPARE NATIONAL EMISSION INVENTORIES. COPENHAGEN, DENMARK: EUROPEAN ENVIRONMENTAL AGENCY (EEA); 2016. AVAILABLE FROM: HTTP://WWW.EEA.EUROPA.EU/PUBLICATIONS/EMEP-EEA-GUIDEBOOK-2016/PART-B-SECTORAL-GUIDANCE-CHAPTERS/5-WASTE; UNECE. THE 1998 PROTOCOL ON PERSISTENT ORGANIC POLLUTANTS, INCLUDING THE AMENDMENTS ADOPTED BY THE PARTIES ON 18 DECEMBER 2009. UNITED NATIONS ECONOMIC COMMISSION FOR EUROPE (UNECE); 2010. AVAILABLE FROM: HTTP://WWW.UNECE.ORG/FILEADMIN/DAM/ENV/LRTAP/FULLTEXT/ECE.EB.AIR.104.E.PDF; FOEN. SWITZERLAND’S INFORMATIVE INVENTORY REPORT 2015 (IIR) SUBMISSION UNDER THE UNECE CONVENTION ON LONG-RANGE TRANSBOUNDARY AIR POLLUTION. FEDERAL OFFICE FOR THE ENVIRONMENT (FOEN); 2015.; CUI S, 2014, SCI TOTAL ENVIRON, V533, P247, DOI 10.1016/J.SCITOTENV.2015.06.144; HU D, 2009, ENVIRON SCI TECHNOL, V44, P2822, DOI 10.1021/ES902413K; BREIVIK K, 2002, SCI TOTAL ENVIRON, V290, P199, DOI 10.1016/S0048-9697(01)01076-2; BREIVIK K, 2006, SCI TOTAL ENVIRON, V377, P296, DOI 10.1016/J.SCITOTENV.2007.02.026; VAN DEN BERG M, 1998, ENVIRON HEALTH PERSPECT, V106, P775, DOI 10.1289/EHP.98106775; VAN DEN BERG M, 2006, TOXICOL SCI, V93, P223, DOI 10.1093/TOXSCI/KFL055; FRAME GM, COCHRAN JW, BØWADT SS. COMPLETE PCB CONGENER DISTRIBUTIONS FOR 17 AROCLOR MIXTURES DETERMINED BY 3 HRGC SYSTEMS OPTIMIZED FOR COMPREHENSIVE, QUANTITATIVE, CONGENER-SPECIFIC ANALYSIS. J HIGH RESOLUT CHROMATOGR. 1996;19:657–668. 10.1002/JHRC.1240191202; TANIYASU S, 2005, J ENVIRON SCI HEALTH A TOX HAZARD SUBST ENVIRON ENG, V40, P43, DOI 10.1081/ESE-200033521; BREIVIK K, 2002, SCI TOTAL ENVIRON, V290, P181, DOI 10.1016/S0048-9697(01)01075-0; TAKASUGA T, INOUE T, ISHIDA T, IRELAND P. DETERMINATION OF THE COMPOSITION OF THE COMMERCIAL PCBS: KANECHLOR, CLOPHEN, AROCLOR, CHLOROFEN, AND SOVOL, BY HRGC-HRMS. ORGANOHALOGEN COMPD. 1996;27:391–396.; ERICKSON MD, 2010, ENVIRON SCI POLLUT RES INT, V18, P135, DOI 10.1007/S11356-010-0392-1; HARRAD SJ, 1992, ENVIRON POLLUT, V85, P131, DOI 10.1016/0269-7491(94)90079-5; BUWAL. PRAXISHILFE: PCB-EMISSIONEN BEIM KORROSIONSSCHUTZ. BERN, SWITZERLAND: BUNDESAMT FÜR UMWELT, WALD UND LANDSCHAFT; 2000.; UNECE. GUIDELINES FOR REPORTING EMISSIONS AND PROJECTIONS DATA UNDER THE CONVENTION ON LONG-RANGE TRANSBOUNDARY AIR POLLUTION (ECE/EB.AIR/128). UNITED NATIONS ECONOMIC COMMISSION FOR EUROPE (UNECE); 2015. AVAILABLE FROM: HTTP://WWW.UNECE.ORG/FILEADMIN/DAM/ENV/DOCUMENTS/2015/AIR/EB/ENGLISH.PDF; BUWAL. ZUR KONTROLLE UND ENTSORGUNG POLYCHLORIERTER BIPHENYLE IN DER SCHWEIZ. SCHRIFTENREIHE UMWELTSCHUTZ NR. 25. BERN, SWITZERLAND: BUNDESAMT FÜR UMWELTSCHUTZ; 1984.; BUWAL. SCHUTZ VOR UMWELTSCHÄDEN DURCH PCB-HALTIGE KONDENSATOREN UND TRANSFORMATOREN. SCHRIFTENREIHE UMWELTSCHUTZ NR. 90. BERN, SWITZERLAND: BUNDESAMT FÜR UMWELTSCHUTZ; 1988.; DE VOOGT P, BRINKMAN UAT. PRODUCTION, PROPERTIES AND USAGE OF POLYCHLORINATED BIPHENYLS. IN: HALOGENATED BIPHENYLS, TERPHENYLS, NAPHTALENES, DIBENZODIOXINS RELAT. PROD.; 1989.; GLÜGE J, 2015, SCI TOTAL ENVIRON, V550, P1152, DOI 10.1016/J.SCITOTENV.2016.01.097; STEINLIN C, 2014, ENVIRON SCI TECHNOL, V48, P7849, DOI 10.1021/ES501793H; STEINLIN C, 2015, ENVIRON SCI TECHNOL, V49, P14092, DOI 10.1021/ACS.EST.5B03304; UBL S, SCHERINGER M, STOHL A, BURKHART JF, HUNGERBÜHLER K. PRIMARY SOURCE REGIONS OF POLYCHLORINATED BIPHENYLS (PCBS) MEASURED IN THE ARCTIC. ATMOS ENVIRON. 2012;62(0):391–399. 10.1016/J.ATMOSENV.2012.07.061; MACLEOD M, 2005, ENVIRON SCI TECHNOL, V39, P6749, DOI 10.1021/ES048426R; ARNET R, KUHN E, NÄF U. KONDENSATOREN VERZEICHNIS—ERKENNUNG UND ENTSORGUNG PCB-HALTIGER KONDENSATOREN; 2011. AVAILABLE FROM: HTTP://WWW.CHEMSUISSE.CH/DE/FACHLICHES/PCB; TREMP J, WEGMANN L. STAND DES’PHASE-OUT’ VON PCB IN DER SCHWEIZ: ERGEBNISSE EINER UNTERSUCHUNG ÜBER PCB-RESERVOIRE UND MASSNAHMEN FÜR DIE BESCHLEUNIGTE UND SICHERE ENTSORGUNG. ARBEITSEXEMPLAR FÜR DIE SCHRIFTENREIHE UMWELT. BERN, SWITZERLAND; 2001.; BARGHOORN M, BAUER RK, GÖSSELE P. ABSCHLUSSBERICHT ZUM FORSCHUNGSVORHABEN PCB-KLEINKONDENSATOREN. ARBEITSGRUPPE UMWELTSTATISTIK-ARGUS AN DER TECHNISCHEN UNIVERSITÄT BERLIN. BERLIN, GERMANY; 1988.; KUHN E, ARNET R. PCB IN VORSCHALTGERÄTEN VON FLUORESZENZLAMPEN – EINE BILANZIERUNG. KANTONALES LABOR KANTON AARGAU. AARAU, SWITZERLAND; 1998.; BUWAL. RICHTLINIE PCB-HALTIGE FUGENDICHTUNGSMASSEN – BEURTEILUNG DES HANDLUNGSBEDARFS UND EMPFEHLUNGEN FÜR DAS VORGEHEN BEI BAUTEN. BERN, SWITZERLAND: BUNDESAMT FÜR UMWELT, WALD UND LANDSCHAFT; 2003.; KOHLER M, 2005, ENVIRON SCI TECHNOL, V39, P1967, DOI 10.1021/ES048632Z; BUWAL. DIFFUSE QUELLEN VON PCB IN DER SCHWEIZ. SCHRIFTENREIHE UMWELT NR. 229. BERN, SWITZERLAND: BUNDESAMT FÜR UMWELT, WALD UND LANDSCHAFT; 1994.; ABBASI G, 2014, ENVIRON SCI TECHNOL, V49, P1521, DOI 10.1021/ES504007V; DAVIS J, GEYER R, LEY J, HE J, CLIFT R, KWAN A, ET AL. TIME-DEPENDENT MATERIAL FLOW ANALYSIS OF IRON AND STEEL IN THE UK – PART 2. SCRAP GENERATION AND RECYCLING. RESOUR CONSERV RECYCL. 2007;51:118–140. 10.1016/J.RESCONREC.2006.08.007; DIEFENBACHER PS, 2015, ENVIRON SCI TECHNOL, V50, P232, DOI 10.1021/ACS.EST.5B04626; HAUSER A. THESENPAPIER: ENTSORGUNG BESCHICHTETER STAHLSCHROTT. BUNDESAMT FÜR UMWELT (BAFU). HOLINGER AG. BERN/LUZERN, SWITZERLAND; 2014.; MACKAY D. POLYCHLORINATED BIPHENYLS (PCBS). IN: HANDB. PHYS. PROP. ENVIRON. FATE ORG. CHEM.. 2ND ED.; 2006. AVAILABLE FROM: HTTP://WWW.CRCNETBASE.COM/DOI/PDFPLUS/10.1201/9781420044393.CH7; WERMEILLE C. PERSONAL COMMUNICATION, JULY 2016; 2016.; IFEU. ERMITTLUNG VON EMISSIONEN UND MINDERUNGSMAßNAHMEN FÜR PERSISTENTE ORGANISCHE SCHADSTOFFE IN DER BUNDESREPUBLICK DEUTSCHLAND (UBA-FB 98-115). INSTITUT FÜR ENERGIE- UND UMWELTFORSCHUNG HEIDELBERG; 1998. AVAILABLE FROM: HTTP://WWW.DIOXINDB.DE/DOKUMENTE/UBA_1998_TEXTE_74-98_POPS_INVENTARE_PCB_SCCP_HCBD_GEDRUCKT.PDF; MACLEOD M, 2002, ENVIRON TOXICOL CHEM, V21, P700; HELTON JC, DAVIS FJ. LATIN HYPERCUBE SAMPLING AND THE PROPAGATION OF UNCERTAINTY IN ANALYSES OF COMPLEX SYSTEMS. RELIAB ENG SYST SAF. 2003;81(1):23–69. 10.1016/S0951-8320(03)00058-9; BOGDAL C, 2014, ENVIRON SCI TECHNOL, V48, P482, DOI 10.1021/ES4044352; DIEFENBACHER PS, 2015, ENVIRON SCI TECHNOL, V49, P2199, DOI 10.1021/ES505242D; GRONTMIJ. SURVEY OF PCB IN MATERIALS AND INDOOR AIR—CONSOLIDATED REPORT. GRONTMIJ/COWI CONSORTIUM; 2013.; SRF. LETZTE CORONADO; 2013. AVAILABLE FROM: HTTP://WWW.SRF.CH/NEWS/FLUGHAFEN-ZUERICH/VIDEOS/LETZTE-CORONADO; FOEN. PAINTS AND VARNISHES; 2016. AVAILABLE FROM: HTTPS://WWW.BAFU.ADMIN.CH/BAFU/EN/HOME/TOPICS/CHEMICALS/INFO-SPECIALISTS/CHEMICALS--REGULATIONS-AND-PROCEDURES/PCB/PAINTS-AND-VARNISHES.HTML; BOGDAL C, 2016, ENVIRON POLLUT, V220, P891, DOI 10.1016/J.ENVPOL.2016.10.073
#> 3 <NA>pubmedR is designed to work seamlessly with bibliometrix and its Shiny interface biblioshiny.
library(bibliometrix)
# Convert and analyze
M <- convert2df(D, dbsource = "pubmed", format = "api")
results <- biblioAnalysis(M)
summary(results)
# Or launch the interactive dashboard
biblioshiny()The data frame produced by pmApi2df() uses the same field tags as
bibliometrix, so it can be directly used with all bibliometrix
functions: biblioAnalysis(), biblioNetwork(), thematicMap(),
conceptualStructure(), and more.
The typical pubmedR workflow follows these steps. Use pmCollect() to
run the full pipeline in one call, or use the individual functions for
fine-grained control:
pmCollect() Individual functions
(one step) (step by step)
+-------------------+
+----------------+ | pmQueryBuild() |
| | | Build query |
| pmCollect() | +---------+---------+
| | |
| Builds query, | v
| counts records,| +-------------------+
| downloads, | | pmQueryTotalCount()|
| converts, | | Check result count|
| enriches (opt) | +---------+---------+
| | |
+-------+--------+ +--------------+--------------+
| | |
| v v
| +-------------------+ +-------------------+
| | pmApiRequest() | | pmFetchById() |
| | Search & download | | Download by PMID |
| +---------+---------+ +---------+---------+
| | |
| +-------------+---------------+
| |
| v
| +-------------------+
| | pmApi2df() |
| | Convert to df |
| +---------+---------+
| |
| v
| +-------------------+
| | pmEnrichCitations()|
| | Add TC & CR |
| +---------+---------+
| |
+------------------------------------+
|
v
+-------------------+
| bibliometrix |
| Analyze & explore |
+-------------------+
PubMed is a free search engine maintained by the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM). It provides access to over 36 million citations and abstracts of biomedical literature from MEDLINE, life science journals, and online books.
pubmedR uses the NCBI E-utilities API, which provides programmatic access to PubMed data including:
- ESearch: Search and retrieve a list of matching record IDs
- EFetch: Download full records in XML format
- ELink: Find related records (citations, references)
If you use pubmedR in your research, please cite it as:
citation("pubmedR")Aria, M. (2023). pubmedR: Gathering Metadata About Publications, Grants, Clinical Trials from PubMed Database. R package. https://github.com/massimoaria/pubmedR
- Report bugs or request features at: https://github.com/massimoaria/pubmedR/issues
- For bibliometric analysis: https://www.bibliometrix.org
- NCBI API documentation: https://www.ncbi.nlm.nih.gov/books/NBK25500/