Index coverage
Europe PMC covers life science literature and gives access to open access full texts. Europe PMC ingests all PubMed content and extends its index with other sources, including Agricola, a bibliographic database of citations to the agricultural literature, or Biological Patents.
Index coverage
For more background, see:
Europe PMC: a full-text literature database for the life sciences and platform for innovation. (2014). Nucleic Acids Research, 43(D1), D1042–D1048. http://doi.org/10.1093/nar/gku1061
The latest development version can be installed using devtools package:
require(devtools)
install_github("ropensci/europepmc")The search covers both metadata (e.g. abstracts or title) and full texts. To build your query, please refer to the comprehensive guidance on how to search Europe PMC: http://europepmc.org/help. Simply provide your query in the Europe PMC search syntax to epmc_search().
The search function helps to get a general overview about additional information types that are offered by Europe PMC and which can be retrieved through other europepmc-functions. Columns inform whether open access full texts (isOpenAccess), cross-links to other EBI databases (hasDbCrossReferences), text-mined terms (hasTextMinedTerms) or references (hasReferences) are available.
By default, epmc_search returns 25 records. To adjust the limit, simply use the limit parameter.
Either list of publication ids (id_list = TRUE) or key metadata information (id_list = FALSE, default option) are returned.
For instance, search for abstracts and full texts that mention Gabi-Kat:
library(europepmc)
my_data <- epmc_search(query = 'Gabi-Kat')
# first six records
head(my_data)
#> id source pmid pmcid doi
#> 1 27117628 MED 27117628 PMC4846993 10.1038/srep24971
#> 2 26842807 MED 26842807 PMC4740857 10.1038/srep20309
#> 3 26930070 MED 26930070 PMC4773003 10.1371/journal.pone.0150254
#> 4 26957563 MED 26957563 PMC4861014 10.1093/jxb/erw096
#> 5 27216227 MED 27216227 PMC4890181 10.1038/ncomms11654
#> 6 27064270 MED 27064270 PMC4814454 10.3389/fpls.2016.00405
#> title
#> 1 Cancer-specific binary expression system activated in mice by bacteriophage HK022 Integrase.
#> 2 Precocious leaf senescence by functional loss of PROTEIN S-ACYL TRANSFERASE14 involves the NPR1-dependent salicylic acid signaling.
#> 3 The Arabidopsis Domain of Unknown Function 1218 (DUF1218) Containing Proteins, MODIFYING WALL LIGNIN-1 and 2 (At1g31720/MWL-1 and At4g19370/MWL-2) Function Redundantly to Alter Secondary Cell Wall Lignin Content.
#> 4 SLTAB2 is the paramutated SULFUREA locus in tomato.
#> 5 A voltage-dependent chloride channel fine-tunes photosynthesis in plants.
#> 6 Photosystem II Repair and Plant Immunity: Lessons Learned from Arabidopsis Mutant Lacking the THYLAKOID LUMEN PROTEIN 18.3.
#> authorString
#> 1 Elias A, Spector I, Sogolovsky-Bard I, Gritsenko N, Rask L, Mainbakh Y, Zilberstein Y, Yagil E, Kolot M.
#> 2 Zhao XY, Wang JG, Song SJ, Wang Q, Kang H, Zhang Y, Li S.
#> 3 Mewalal R, Mizrachi E, Coetzee B, Mansfield SD, Myburg AA.
#> 4 Gouil Q, Novák O, Baulcombe DC.
#> 5 Herdean A, Teardo E, Nilsson AK, Pfeil BE, Johansson ON, Ünnep R, Nagy G, Zsiros O, Dana S, Solymosi K, Garab G, Szabó I, Spetea C, Lundin B.
#> 6 Järvi S, Isojärvi J, Kangasjärvi S, Salojärvi J, Mamedov F, Suorsa M, Aro EM.
#> journalTitle journalVolume pubYear journalIssn pageInfo
#> 1 Sci Rep 6 2016 2045-2322 24971
#> 2 Sci Rep 6 2016 2045-2322 20309
#> 3 PLoS One 11 2016 1932-6203 e0150254
#> 4 J Exp Bot 67 2016 0022-0957 2655-2664
#> 5 Nat Commun 7 2016 2041-1723 11654
#> 6 Front Plant Sci 7 2016 1664-462x 405
#> pubType
#> 1 journal article; research-article
#> 2 journal article; research support, non-u.s. gov't; research-article
#> 3 journal article; research support, non-u.s. gov't; research-article
#> 4 journal article; research-article
#> 5 journal article; research-article
#> 6 journal article; research-article
#> isOpenAccess inEPMC inPMC hasPDF hasBook hasSuppl citedByCount
#> 1 Y Y N Y N N 0
#> 2 Y Y N Y N N 1
#> 3 Y Y N Y N N 0
#> 4 Y Y N Y N Y 1
#> 5 Y Y N Y N N 0
#> 6 Y Y N Y N N 0
#> hasReferences hasTextMinedTerms hasDbCrossReferences hasLabsLinks
#> 1 Y Y N Y
#> 2 Y Y N Y
#> 3 Y Y N Y
#> 4 Y Y N Y
#> 5 Y Y N Y
#> 6 Y Y N Y
#> epmcAuthMan hasTMAccessionNumbers luceneScore issue
#> 1 N N NaN <NA>
#> 2 N N NaN <NA>
#> 3 N N NaN 3
#> 4 N N NaN 9
#> 5 N N NaN <NA>
#> 6 N N NaN <NA>Get PLOS Genetics (ISSN:1553-7404) articles that cross-reference EMBL:
my_data <- epmc_search(query = 'ISSN:1553-7404 HAS_EMBL:y')
head(my_data)
#> id source pmid pmcid doi
#> 1 27149082 MED 27149082 PMC4858218 10.1371/journal.pgen.1006030
#> 2 27203426 MED 27203426 PMC4874600 10.1371/journal.pgen.1006063
#> 3 26982327 MED 26982327 PMC4794157 10.1371/journal.pgen.1005920
#> 4 27120580 MED 27120580 PMC4847869 10.1371/journal.pgen.1005987
#> 5 27327578 MED 27327578 PMC4915694 10.1371/journal.pgen.1006110
#> 6 27082250 MED 27082250 PMC4833346 10.1371/journal.pgen.1005954
#> title
#> 1 Germline Defects Caused by Smed-boule RNA-Interference Reveal That Egg Capsule Deposition Occurs Independently of Fertilization, Ovulation, Mating, or the Presence of Gametes in Planarian Flatworms.
#> 2 Antimicrobial Functions of Lactoferrin Promote Genetic Conflicts in Ancient Primates and Modern Humans.
#> 3 Hybrid Dysgenesis in Drosophila simulans Associated with a Rapid Invasion of the P-Element.
#> 4 An Indel Polymorphism in the MtnA 3' Untranslated Region Is Associated with Gene Expression Variation and Local Adaptation in Drosophila melanogaster.
#> 5 Genetic Dissection of Sexual Reproduction in a Primary Homothallic Basidiomycete.
#> 6 Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding.
#> authorString
#> 1 Steiner JK, Tasaki J, Rouhana L.
#> 2 Barber MF, Kronenberg Z, Yandell M, Elde NC.
#> 3 Hill T, Schlötterer C, Betancourt AJ.
#> 4 Catalán A, Glaser-Schmitt A, Argyridou E, Duchen P, Parsch J.
#> 5 David-Palma M, Sampaio JP, Gonçalves P.
#> 6 Vij S, Kuhl H, Kuznetsova IS, Komissarov A, Yurchenko AA, Van Heusden P, Singh S, Thevasagayam NM, Prakki SR, Purushothaman K, Saju JM, Jiang J, Mbandi SK, Jonas M, Hin Yan Tong A, Mwangi S, Lau D, Ngoh SY, Liew WC, Shen X, Hon LS, Drake JP, Boitano M, Hall R, Chin CS, Lachumanan R, Korlach J, Trifonov V, Kabilov M, Tupikin A, Green D, Moxon S, Garvin T, Sedlazeck FJ, Vurture GW, Gopalapillai G, Kumar Katneni V, Noble TH, Scaria V, Sivasubbu S, Jerry DR, O'Brien SJ, Schatz MC, Dalmay T, Turner SW, Lok S, Christoffels A, Orbán L.
#> journalTitle issue journalVolume pubYear journalIssn pageInfo
#> 1 PLoS Genet 5 12 2016 1553-7390 e1006030
#> 2 PLoS Genet 5 12 2016 1553-7390 e1006063
#> 3 PLoS Genet 3 12 2016 1553-7390 e1005920
#> 4 PLoS Genet 4 12 2016 1553-7390 e1005987
#> 5 PLoS Genet 6 12 2016 1553-7390 e1006110
#> 6 PLoS Genet 4 12 2016 1553-7390 e1005954
#> pubType
#> 1 journal article; research-article
#> 2 journal article; research-article
#> 3 journal article; research support, non-u.s. gov't; research-article
#> 4 journal article; research-article
#> 5 journal article; research-article
#> 6 journal article; research-article
#> isOpenAccess inEPMC inPMC hasPDF hasBook hasSuppl citedByCount
#> 1 Y Y N Y N N 0
#> 2 Y Y N Y N N 0
#> 3 Y Y N Y N N 1
#> 4 Y Y N Y N N 0
#> 5 Y Y N Y N N 0
#> 6 Y Y N Y N N 0
#> hasReferences hasTextMinedTerms hasDbCrossReferences hasLabsLinks
#> 1 Y Y Y Y
#> 2 Y Y Y Y
#> 3 Y Y Y Y
#> 4 Y Y Y Y
#> 5 N Y Y Y
#> 6 Y Y Y Y
#> epmcAuthMan hasTMAccessionNumbers luceneScore
#> 1 N N NaN
#> 2 N Y NaN
#> 3 N Y NaN
#> 4 N Y NaN
#> 5 N N NaN
#> 6 N Y NaNCount hits before with epmc_hits to define limit. For example, get list of ids that represent articles referencing DataCite DOIs:
query <- "ACCESSION_TYPE:doi"
epmc_hits(query)
#> [1] 5402
# set limit to 10 records
my_data <- epmc_search(query = "ACCESSION_TYPE:doi", limit = 10,
id_list = TRUE)
head(my_data)
#> id source pmid pmcid
#> 1 27019208 MED 27019208 PMC4809487
#> 2 26955653 MED 26955653 PMC4761700
#> 3 27064844 MED 27064844 PMC4814564
#> 4 27143036 MED 27143036 PMC4855483
#> 5 26977150 MED 26977150 PMC4762996
#> 6 26978783 MED 26978783 PMC4792385
attr(my_data, "hit_count")
#> [1] 5402Use ORCID to search for personal publications:
my_data <- epmc_search(query = 'AUTHORID:"0000-0002-7635-3473"')
attr(my_data, "hit_count")
#> [1] 127You may also want to include synonyms when searching Europe PMC. If synonym = TRUE MeSH and UniProt synonyms are searched as well.
my_data <- epmc_search("aspirin", synonym = TRUE)
attr(my_data, "hit_count")
#> [1] 112983
my_data <- epmc_search("aspirin", synonym = FALSE)
attr(my_data, "hit_count")
#> [1] 105706In addition to key metadata, epmc_details also returns full metadata providing more comprehensive information on the article-level. By default, PubMed / Medline index is searched.
epmc_details(ext_id = "24270414")
#> $basic
#> id source pmid pmcid doi
#> 1 24270414 MED 24270414 PMC3859427 10.1172/jci73168
#> title authorString
#> 1 ADCK4 "reenergizes" nephrotic syndrome. Malaga-Dieguez L, Susztak K.
#> pageInfo
#> 1 4996-4999
#> abstractText
#> 1 Steroid-resistant nephrotic syndrome has a poor prognosis and often leads to end-stage renal disease development. In this issue of the JCI, Ashraf and colleagues used exome sequencing to identify mutations in the aarF domain containing kinase 4 (ADCK4) gene that cause steroid-resistant nephrotic syndrome. Patients with ADCK4 mutations had lower coenzyme Q10 levels, and coenzyme Q10 supplementation ameliorated renal disease in a patient with this particular mutation, suggesting a potential therapy for patients with steroid-resistant nephrotic syndrome with ADCK4 mutations.
#> language pubModel isOpenAccess inEPMC inPMC hasPDF hasBook
#> 1 eng Print-Electronic N Y Y Y N
#> hasSuppl citedByCount hasReferences hasTextMinedTerms
#> 1 N 1 Y Y
#> hasDbCrossReferences hasLabsLinks epmcAuthMan hasTMAccessionNumbers
#> 1 N Y N N
#> dateOfCompletion dateOfCreation dateOfRevision electronicPublicationDate
#> 1 2014-02-04 2013-12-02 2015-07-10 2013-11-25
#> firstPublicationDate luceneScore
#> 1 2013-11-25 NaN
#>
#> $author_details
#> fullName firstName lastName initials
#> 1 Malaga-Dieguez L Laura Malaga-Dieguez L
#> 2 Susztak K Katalin Susztak K
#>
#> $journal_info
#> issue volume journalIssueId dateOfPublication monthOfPublication
#> 1 12 123 2099360 2013 Dec 12
#> yearOfPublication printPublicationDate
#> 1 2013 2013-12-01
#> journal.title journal.medlineAbbreviation
#> 1 The Journal of clinical investigation J Clin Invest
#> journal.essn journal.issn journal.isoabbreviation journal.nlmid
#> 1 1558-8238 0021-9738 J. Clin. Invest. 7802877
#>
#> $ftx
#> availability availabilityCode documentStyle site
#> 1 Free F pdf Europe_PMC
#> 2 Free F html Europe_PMC
#> 3 Free F pdf PubMedCentral
#> 4 Free F html PubMedCentral
#> 5 Subscription required S doi DOI
#> url
#> 1 http://europepmc.org/articles/PMC3859427?pdf=render
#> 2 http://europepmc.org/articles/PMC3859427
#> 3 http://www.pubmedcentral.nih.gov/picrender.fcgi?tool=EBI&pubmedid=24270414&action=stream&blobtype=pdf
#> 4 http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=24270414
#> 5 http://dx.doi.org/10.1172/JCI73168
#>
#> $chemical
#> name registryNumber
#> 1 Ubiquinone 1339-63-5
#> 2 Protein Kinases EC 2.7.-
#> 3 aarF domain containing kinase 4, human EC 2.7.-
#> 4 coenzyme Q10 EJ27X76M46
#>
#> $mesh_topic
#> majorTopic_YN descriptorName
#> 1 N Animals
#> 2 N Humans
#> 3 N Nephrotic Syndrome
#> 4 N Ubiquinone
#> 5 N Protein Kinases
#>
#> $comments
#> id source reference type
#> 1 24270420 MED J Clin Invest. 2013 Dec;123(12):5179-89 Comment on
#> orderIn
#> 1 19
#>
#> $grants
#> grantId agency acronym orderIn
#> 1 R01DK076077 NIDDK NIH HHS DK 0Show author details including ORCID:
my_data <- epmc_details(ext_id = "14756321")
my_data$author_details
#> fullName firstName lastName initials authorId.type
#> 1 Rosso MG Mario G Rosso MG <NA>
#> 2 Li Y Yong Li Y <NA>
#> 3 Strizhov N Nicolai Strizhov N <NA>
#> 4 Reiss B Bernd Reiss B ORCID
#> 5 Dekker K Koen Dekker K <NA>
#> 6 Weisshaar B Bernd Weisshaar B ORCID
#> authorId.value
#> 1 <NA>
#> 2 <NA>
#> 3 <NA>
#> 4 0000-0002-2521-4000
#> 5 <NA>
#> 6 0000-0002-7635-3473Citing publications from the Europe PMC index can be retrieved like this:
my_cites <- epmc_citations("9338777")
head(my_cites)
#> id source
#> 1 9525633 MED
#> 2 9811736 MED
#> 3 9728986 MED
#> 4 9728985 MED
#> 5 9728987 MED
#> 6 10590090 MED
#> citationType
#> 1 Journal Article
#> 2 Journal Article; Research Support, Non-U.S. Gov't
#> 3 Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, P.H.S.
#> 4 Journal Article; Research Support, Non-U.S. Gov't
#> 5 Case Reports; Journal Article; Research Support, Non-U.S. Gov't
#> 6 Journal Article; Research Support, Non-U.S. Gov't
#> title
#> 1 Type C retrovirus released from porcine primary peripheral blood mononuclear cells infects human cells.
#> 2 Host range and interference studies of three classes of pig endogenous retrovirus.
#> 3 No evidence of infection with porcine endogenous retrovirus in recipients of porcine islet-cell xenografts.
#> 4 Expression of pig endogenous retrovirus by primary porcine endothelial cells and infection of human cells.
#> 5 No evidence of pig DNA or retroviral infection in patients with short-term extracorporeal connection to pig kidneys.
#> 6 Extended analysis of the in vitro tropism of porcine endogenous retrovirus.
#> authorString
#> 1 Wilson CA, Wong S, Muller J, Davidson CE, Rose TM, Burd P.
#> 2 Takeuchi Y, Patience C, Magre S, Weiss RA, Banerjee PT, Le Tissier P, Stoye JP.
#> 3 Heneine W, Tibell A, Switzer WM, Sandstrom P, Rosales GV, Mathews A, Korsgren O, Chapman LE, Folks TM, Groth CG.
#> 4 Martin U, Kiessig V, Blusch JH, Haverich A, von der Helm K, Herden T, Steinhoff G.
#> 5 Patience C, Patton GS, Takeuchi Y, Weiss RA, McClure MO, Rydberg L, Breimer ME.
#> 6 Wilson CA, Wong S, VanBrocklin M, Federspiel MJ.
#> journalAbbreviation pubYear volume issue pageInfo citedByCount
#> 1 J. Virol. 1998 72 4 3082-3087 193
#> 2 J. Virol. 1998 72 12 9986-9991 190
#> 3 Lancet 1998 352 9129 695-699 167
#> 4 Lancet 1998 352 9129 692-694 156
#> 5 Lancet 1998 352 9129 699-701 144
#> 6 J. Virol. 2000 74 1 49-56 108
attr(my_cites, "hit_count")
#> [1] 192Please note, that citation counts are often smaller than those held by toll- access services such as Web of Science or Scopus because the number of reference sections indexed for Europe PMC considerably differs due to the lack of full text accessibility.
Europe PMC indexes more than 5 million reference sections.
epmc_refs("PMC3166943", data_src = "pmc")
#> id source citationType
#> 1 10802651 MED JOURNAL ARTICLE
#> 2 <NA> <NA> <NA>
#> 3 18077472 MED JOURNAL ARTICLE
#> 4 15642104 MED JOURNAL ARTICLE
#> 5 18460184 MED JOURNAL ARTICLE
#> 6 17989687 MED JOURNAL ARTICLE
#> 7 20848809 MED JOURNAL ARTICLE
#> 8 20139945 MED JOURNAL ARTICLE
#> 9 <NA> <NA> <NA>
#> 10 17267433 MED JOURNAL ARTICLE
#> 11 15199967 MED JOURNAL ARTICLE
#> 12 14681407 MED JOURNAL ARTICLE
#> 13 16756499 MED JOURNAL ARTICLE
#> 14 16959967 MED JOURNAL ARTICLE
#> 15 16518471 MED JOURNAL ARTICLE
#> 16 11901169 MED JOURNAL ARTICLE
#> 17 15892874 MED JOURNAL ARTICLE
#> 18 <NA> <NA> <NA>
#> title
#> 1 Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
#> 2 The Gene Ontology (GO) project in 2008
#> 3 Biomedical ontologies: a functional perspective.
#> 4 Gene Ontology: looking backwards and forwards.
#> 5 Gene Ontology annotations: what they mean and where they come from.
#> 6 The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.
#> 7 Documenting the emergence of bio-ontologies: or, why researching bioinformatics requires HPSSB.
#> 8 Ontology engineering.
#> 9 Minutes of Gene Ontology 2005 Meeting
#> 10 Ontology development for biological systems: immunology.
#> 11 Innate immunity in plants and animals: striking similarities and obvious differences.
#> 12 The Gene Ontology (GO) database and informatics resource.
#> 13 Dynamic filaments of the bacterial cytoskeleton.
#> 14 The bacterial cytoskeleton.
#> 15 Cytoskeletal components of an invasion machine--the apical complex of Toxoplasma gondii.
#> 16 A novel polymer of tubulin forms the conoid of Toxoplasma gondii.
#> 17 Relations in biomedical ontologies.
#> 18 The Gene Ontology in 2010: extensions and refinements
#> authorString
#> 1 Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G.
#> 2 AUTHOR UNKNOWN
#> 3 Rubin DL, Shah NH, Noy NF.
#> 4 Lewis SE.
#> 5 Hill DP, Smith B, McAndrews-Hill MS, Blake JA.
#> 6 Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ; OBI Consortium, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S.
#> 7 Leonelli S.
#> 8 Alterovitz G, Xiang M, Hill DP, Lomax J, Liu J, Cherkassky M, Dreyfuss J, Mungall C, Harris MA, Dolan ME, Blake JA, Ramoni MF.
#> 9 AUTHOR UNKNOWN
#> 10 Diehl AD, Lee JA, Scheuermann RH, Blake JA.
#> 11 Nurnberger T, Brunner F, Kemmerling B, Piater L.
#> 12 Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R; Gene Ontology Consortium.
#> 13 Michie KA, Lowe J.
#> 14 Shih YL, Rothfield L.
#> 15 Hu K, Johnson J, Florens L, Fraunholz M, Suravajjala S, DiLullo C, Yates J, Roos DS, Murray JM.
#> 16 Hu K, Roos DS, Murray JM.
#> 17 Smith B, Ceusters W, Klagges B, Kohler J, Kumar A, Lomax J, Mungall C, Neuhaus F, Rector AL, Rosse C.
#> 18 AUTHOR UNKNOWN
#> journalAbbreviation issue pubYear volume pageInfo
#> 1 Nat. Genet. 1 2000 25 25-29
#> 2 <NA> <NA> 2007 <NA> 1-5
#> 3 Brief. Bioinformatics 1 2008 9 75-90
#> 4 Genome Biol. 1 2005 6 103
#> 5 BMC Bioinformatics <NA> 2008 9 Suppl 5 S2
#> 6 Nat. Biotechnol. 11 2007 25 1251-1255
#> 7 Hist Philos Life Sci 1 2010 32 105-125
#> 8 Nat. Biotechnol. 2 2010 28 128-130
#> 9 <NA> <NA> 0 <NA> <NA>
#> 10 Bioinformatics 7 2007 23 913-915
#> 11 Immunol. Rev. <NA> 2004 198 249-266
#> 12 Nucleic Acids Res. Database issue 2004 32 D258-61
#> 13 Annu. Rev. Biochem. <NA> 2006 75 467-492
#> 14 Microbiol. Mol. Biol. Rev. 3 2006 70 729-754
#> 15 PLoS Pathog. 2 2006 2 e13
#> 16 J. Cell Biol. 6 2002 156 1039-1050
#> 17 Genome Biol. 5 2005 6 R46
#> 18 <NA> 38 Database 2010 <NA> D331-D335
#> citedOrder match essn issn publicationTitle
#> 1 1 Y 1546-1718 1061-4036 <NA>
#> 2 2 N <NA> <NA> Nucleic Acids Research
#> 3 3 Y 1477-4054 1467-5463 <NA>
#> 4 4 Y 1474-760X 1474-7596 <NA>
#> 5 5 Y 1471-2105 <NA> <NA>
#> 6 6 Y 1546-1696 1087-0156 <NA>
#> 7 7 Y 1742-6316 0391-9714 <NA>
#> 8 8 Y 1546-1696 1087-0156 <NA>
#> 9 9 N <NA> <NA> <NA>
#> 10 10 Y 1367-4811 1367-4803 <NA>
#> 11 11 Y 1600-065X 0105-2896 <NA>
#> 12 12 Y 1362-4962 0305-1048 <NA>
#> 13 13 Y 1545-4509 0066-4154 <NA>
#> 14 14 Y 1098-5557 1092-2172 <NA>
#> 15 15 Y 1553-7374 1553-7366 <NA>
#> 16 16 Y 1540-8140 0021-9525 <NA>
#> 17 17 Y 1474-760X 1474-7596 <NA>
#> 18 18 N <NA> <NA> Nucleic Acids Research
#> externalLink
#> 1 <NA>
#> 2 <NA>
#> 3 <NA>
#> 4 <NA>
#> 5 <NA>
#> 6 <NA>
#> 7 <NA>
#> 8 <NA>
#> 9 http://www.geneontology.org/minutes/20051115_TIGR_Content/20051115_TIGR_Content.pdf
#> 10 <NA>
#> 11 <NA>
#> 12 <NA>
#> 13 <NA>
#> 14 <NA>
#> 15 <NA>
#> 16 <NA>
#> 17 <NA>
#> 18 <NA>Tip: add has_reflist:y to your search string in epmc_search to make sure you only get publications whose reference sections are accessible through Europe PMC.
Cross-links to EBI databases are either manually curated (ENA, InterPro, PDB, IntAct, ChEMBL, ChEBI and ArrayExpress) or automatically gathered through text-mining (European Nucleotide Archive, UniProt, PDB, OMIM, RefSNP, RefSeq, Pfam, InterPro, Ensembl, ArrayExpress and data DOIs).
Before retrieving the links, please check availability and sources first:
epmc_db_count("12368864")
#> dbName count
#> 1 EMBL 10
#> 2 INTERPRO 1
#> 3 UNIPROT 5588Add has_xrefs:y or to your search string in epmc_search to make sure you only get publications with cross-references to EBI databases.
Select database and get links:
epmc_db("12368864", db = "embl")
#> info1 info2
#> 1 AE014187 Plasmodium falciparum 3D7 chromosome 14, complete sequence.
#> 2 AE014186 Plasmodium falciparum 3D7 chromosome 11, complete sequence.
#> 3 LN999943 Plasmodium falciparum 3D7 chromosome 2, complete sequence.
#> 4 AE001362 Plasmodium falciparum 3D7 chromosome 2, complete sequence.
#> 5 LN999947 Plasmodium falciparum 3D7 chromosome 12, complete sequence.
#> 6 AE014185 Plasmodium falciparum 3D7 chromosome 10, complete sequence.
#> 7 LN999944 Plasmodium falciparum 3D7 chromosome 10, complete sequence.
#> 8 LN999945 Plasmodium falciparum 3D7 chromosome 11, complete sequence.
#> 9 LN999946 Plasmodium falciparum 3D7 chromosome 14, complete sequence.
#> 10 AE014188 Plasmodium falciparum 3D7 chromosome 12, complete sequence.
#> info3 info4
#> 1 3291871 10
#> 2 2038337 10
#> 3 947102 10
#> 4 947102 10
#> 5 2271494 10
#> 6 1687655 10
#> 7 1687656 10
#> 8 2038340 10
#> 9 3291936 10
#> 10 2271478 10Text-mined terms that can be accessed via Europe PMC are mapped against controlled vocabularies such as Gene Ontology.
Before retrieving these terms, please check availability and vocabularies first:
epmc_tm_count("25249410")
#> name count
#> 1 accession 1
#> 2 chemical 25
#> 3 disease 1
#> 4 efo 28
#> 5 gene_protein 51
#> 6 go_term 17
#> 7 organism 27Select vocabulary to retrieve the terms:
epmc_tm("25249410", semantic_type = "GO_TERM")
#> term count altName dbName dbId
#> 1 chromosome 25 chromosomes GO 0005694
#> 2 biosynthesis 16 formation, synthesis GO 0009058
#> 3 binding 9 GO 0005488
#> 4 cells 5 cell GO 0005623
#> 5 growth 4 Growth GO 0040007
#> 6 flavonoid biosynthesis 3 GO 0009813
#> 7 gene expression 2 GO 0010467
#> 8 secondary metabolism 2 GO 0019748
#> 9 metabolism 2 GO 0008152
#> 10 defense responses 1 GO 0006952
#> 11 cell cycle control 1 GO 1901987
#> 12 regulation of gene expression 1 GO 0010468
#> 13 glucosinolate biosynthesis 1 GO 0019761
#> 14 cell development 1 GO 0048468
#> 15 root hairs 1 GO 0035618
#> 16 anthocyanin biosynthesis 1 GO 0009718
#> 17 enzyme activities 1 GO 0003824With the External Link services, Europe PMC allows third parties to publish links from Europe PMC to other webpages. Current External Link providers, whose id can be found through Europe PMC’s Advanced Search interface, include Wikipedia, Dryad Digital Repository or the institutional repo of Bielefeld University. For more information, see http://europepmc.org/labslink.
Check availability and number of links:
epmc_lablinks_count("PMC3986813", data_src = "pmc")
#> providerName linksCount
#> 1 EBI Train Online 1
#> 2 Wikipedia 1
#> 3 Publons 1
#> 4 Altmetric 1Get links to PANGEA (lab_id = "1342")
epmc_lablinks("24023770", lab_id = "1342")
#> title
#> 1 Related to: Schewe, I (2010). Biochemical investigation of multicorer sediment profile PS74/106-3. Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, PANGAEA
#> 2 Related to: Schewe, I (2010). Biochemical investigation of multicorer sediment profile PS74/107-2. Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, PANGAEA
#> 3 Related to: Schewe, I (2010). Biochemical investigation of multicorer sediment profile PS74/108-2. Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, PANGAEA
#> 4 Related to: Schewe, I (2010). Biochemical investigation of multicorer sediment profile PS74/109-2. Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, PANGAEA
#> 5 Related to: Schewe, I (2010). Biochemical investigation of multicorer sediment profile PS74/113-2. Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, PANGAEA
#> 6 Related to: Schewe, I (2010). Biochemical investigation of multicorer sediment profile PS74/116-2. Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, PANGAEA
#> 7 Related to: Schewe, I (2010). Biochemical investigation of multicorer sediment profile PS74/118-2. Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, PANGAEA
#> 8 Related to: Schewe, I (2010). Biochemical investigation of multicorer sediment profile PS74/119-2. Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, PANGAEA
#> 9 Related to: Schewe, I (2010). Biochemical investigation of multicorer sediment profile PS74/120-2. Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, PANGAEA
#> 10 Related to: Schewe, I (2010). Biochemical investigation of multicorer sediment profile PS74/121-1. Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, PANGAEA
#> 11 Related to: Schewe, I (2010). Biochemical investigation of multicorer sediment profile PS74/127-2. Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, PANGAEA
#> 12 Related to: Schewe, I (2010). Biochemical investigation of multicorer sediment profile PS74/128-2. Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, PANGAEA
#> 13 Related to: Schewe, I (2010). Biochemical investigation of multicorer sediment profile PS74/129-3. Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, PANGAEA
#> url lab_id lab_name
#> 1 http://dx.doi.org/10.1594/PANGAEA.744673 1342 PANGAEA
#> 2 http://dx.doi.org/10.1594/PANGAEA.744674 1342 PANGAEA
#> 3 http://dx.doi.org/10.1594/PANGAEA.744675 1342 PANGAEA
#> 4 http://dx.doi.org/10.1594/PANGAEA.744676 1342 PANGAEA
#> 5 http://dx.doi.org/10.1594/PANGAEA.744677 1342 PANGAEA
#> 6 http://dx.doi.org/10.1594/PANGAEA.744678 1342 PANGAEA
#> 7 http://dx.doi.org/10.1594/PANGAEA.744679 1342 PANGAEA
#> 8 http://dx.doi.org/10.1594/PANGAEA.744680 1342 PANGAEA
#> 9 http://dx.doi.org/10.1594/PANGAEA.744681 1342 PANGAEA
#> 10 http://dx.doi.org/10.1594/PANGAEA.744682 1342 PANGAEA
#> 11 http://dx.doi.org/10.1594/PANGAEA.744683 1342 PANGAEA
#> 12 http://dx.doi.org/10.1594/PANGAEA.744684 1342 PANGAEA
#> 13 http://dx.doi.org/10.1594/PANGAEA.744685 1342 PANGAEA
#> lab_description
#> 1 Data Publisher for Earth & Environmental Science
#> 2 Data Publisher for Earth & Environmental Science
#> 3 Data Publisher for Earth & Environmental Science
#> 4 Data Publisher for Earth & Environmental Science
#> 5 Data Publisher for Earth & Environmental Science
#> 6 Data Publisher for Earth & Environmental Science
#> 7 Data Publisher for Earth & Environmental Science
#> 8 Data Publisher for Earth & Environmental Science
#> 9 Data Publisher for Earth & Environmental Science
#> 10 Data Publisher for Earth & Environmental Science
#> 11 Data Publisher for Earth & Environmental Science
#> 12 Data Publisher for Earth & Environmental Science
#> 13 Data Publisher for Earth & Environmental ScienceFull texts are in XML format and are only provided for the Open Access subset of Europe PMC. They can be retrieved by the PMCID.
epmc_ftxt("PMC3257301")
#> {xml_document}
#> <article article-type="research-article" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:mml="http://www.w3.org/1998/Math/MathML">
#> [1] <front>\n <journal-meta>\n <journal-id journal-id-type="nlm-ta"> ...
#> [2] <body>\n <sec id="s1">\n <title>Introduction</title>\n <p>Atm ...
#> [3] <back>\n <ack>\n <p>We would like to thank Dr. C. Gourlay and Dr ...Books, fetched through the PMID or the ‘NBK’ book number, can also be loaded as XML into R for further text-mining activities.
epmc_ftxt_book("NBK32884")
#> {xml_document}
#> <book-part book-part-type="toc" id="toc" indexed="true" lang="EN" type="simple" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:mml="http://www.w3.org/1998/Math/MathML">
#> [1] <book-meta>\n <?showBookmeta?>\n <book-id pub-id-type="pmcid">erta ...
#> [2] <book-part-meta>\n <title-group>\n <title>Table of Contents</tit ...
#> [3] <body>\n <list list-type="simple">\n <list-item>\n <?toc-ta ...Please check full-text availability before.
oai to get metadata and full text via Europe PMC’s OAI interface: https://github.com/ropensci/oairentrez to interact with NCBI databases such as PubMed: https://github.com/ropensci/rentrezfulltext package gives access to supplementary material of open access life-science publications in Europe PMC: https://github.com/ropensci/fulltext