DataSpace maintains a curated collection of relevant publications,
which can be accessed through the Publications
page through the app. Some publications include datasets which can
be downloaded as a zip file. DataSpaceR provides an
interface for browsing publications in DataSpace and downloading
publication data where available.
The DataSpaceConnection object includes methods for
browsing and downloading publications and publication data.
The examples below are meant to show abridged console output and are not intended to be exhaustive.
library(DataSpaceR)
library(data.table)
con <- connectDS()
con
#> <DataSpaceConnection>
#> URL: https://dataspace.cavd.org
#> User: jmtaylor@scharp.org
#> Available Studies: 397
#> - 79 studies with data
#> - 5074 subjects
#> - 436354 data points
#> Available Groups: 6
#> Available Publications: 1910
#> - 30 publications with data
#> Available Connection objects:
#> - availableDonors
#> - availableGroups
#> - availableMabMixtures
#> - availableMabs
#> - availablePublications
#> - availableStudies
#> - availableViruses
#> - virusNameMappingTables
#> Available Connection methods:
#> - downloadPublicationData
#> - getDaash
#> - getDonors
#> - getGroups
#> - getMabs
#> - getStudiesThe DataSpaceConnection print method summarizes the
publications and publication data. More details about publications can
be accessed through con$availablePublications.
con$availablePublications
#> publication_id label first_author
#> <char> <char> <char>
#> 1: 1006 <NA> Abbink P
#> 2: 1303 <NA> Abbott RK
#> 3: 1635 <NA> Abernathy ME
#> 4: 1636 <NA> Abernathy ME
#> 5: 1838 <NA> Abernethy NF
#> ---
#> 1906: 276 <NA> deCamp AC
#> 1907: 1029 <NA> van Gils MJ
#> 1908: 1613 <NA> van Schooten J
#> 1909: 1618 <NA> van Schooten J
#> 1910: 1743 <NA> van der Laan L
#> all_authors
#> <char>
#> 1: Abbink P, Maxfield LF, Ng'ang'a D, Borducchi EN, Iampietro MJ, Bricault CA, Teigler JE, Blackmore S, Parenteau L, Wagh K, Handley SA, Zhao G, Virgin HW, Korber B, Barouch DH
#> 2: Abbott RK, Lee JH, Menis S, Skog P, Rossi M, Ota T, Kulp DW, Bhullar D, Kalyuzhniy O, Havenar-Daughton C, Schief WR, Nemazee D, Crotty S
#> 3: Abernathy ME, Gristick HB, Vielmetter J, Keeffe JR, Gnanapragasam PNP, Lee YE, Escolano A, Gautam R, Seaman MS, Martin MA, Nussenzweig MC, Bjorkman PJ
#> 4: Abernathy ME, Dam KMA, Esswein SR, Jette CA, Bjorkman PJ
#> 5: Abernethy NF, McCloskey K, Trahey M, Rinn L, Broder G, Andrasik M, Laborde R, McGhan D, Spendolini S, Marimuthu S, Kanzmeier A, Hanes J, Kublin JG
#> ---
#> 1906: deCamp AC, Rolland M, Edlefsen PT, Sanders-Buell E, Hall B, Magaret CA, Fiore-Gartland AJ, Juraska M, Carpp LN, Karuna ST, Bose M, LePore S, Miller S, O'Sullivan A, Poltavee K, Bai H, Dommaraju K, Zhao H, Wong K, Chen L, Ahmed H, Goodman D, Tay MZ, Gottardo R, Koup RA, Bailer R, Mascola JR, Graham BS, Roederer M, O'Connell RJ, Michael NL, Robb ML, Adams E, D'Souza P, Kublin J, Corey L, Geraghty DE, Frahm N, Tomaras GD, McElrath MJ, Frenkel L, Styrchak S, Tovanabutra S, Sobieszczyk ME, Hammer SM, Kim JH, Mullins JI, Gilbert PB
#> 1907: van Gils MJ, van den Kerkhof TL, Ozorowski G, Cottrell CA, Sok D, Pauthner M, Pallesen J, de Val N, Yasmeen A, de Taeye SW, Schorcht A, Gumbs S, Johanna I, Saye-Francisco K, Liang CH, Landais E, Nie X, Pritchard LK, Crispin M, Kelsoe G, Wilson IA, Schuitemaker H, Klasse PJ, Moore JP, Burton DR, Ward AB, Sanders RW
#> 1908: van Schooten J, Schorcht A, Farokhi E, Umotoy JC, Gao H, van den Kerkhof TLGM, Dorning J, Rijkhold Meesters TG, van der Woude P, Burger JA, Bijl T, Ghalaiyini R, Torrents de la Pena A, Turner HL, Labranche CC, Stanfield RL, Sok D, Schuitemaker H, Montefiori DC, Burton DR, Ozorowski G, Seaman MS, Wilson IA, Sanders RW, Ward AB, van Gils MJ
#> 1909: van Schooten J, Farokhi E, Schorcht A, van den Kerkhof TLGM, Gao H, van der Woude P, Burger JA, Rijkhold Meesters TG, Bijl T, Ghalaiyini R, Turner HL, Dorning J, van Schaik BDC, van Kampen AHC, Labranche CC, Stanfield RL, Sok D, Montefiori DC, Burton DR, Seaman MS, Ozorowski G, Wilson IA, Sanders RW, Ward AB, van Gils MJ
#> 1910: van der Laan L, Zhang W, Gilbert PB
#> title
#> <char>
#> 1: Construction and evaluation of novel rhesus monkey adenovirus vaccine vectors
#> 2: Precursor frequency and affinity determine B Cell competitive fitness in germinal centers, tested with germline-targeting HIV vaccine immunogens
#> 3: Antibody elicited by HIV-1 immunogen vaccination in macaques displaces env fusion peptide and destroys a neutralizing epitope
#> 4: How antibodies recognize pathogenic viruses: Structural correlates of antibody neutralization of HIV-1, SARS-CoV-2, and Zika
#> 5: Rapid development of a registry to accelerate COVID-19 vaccine clinical trials
#> ---
#> 1906: Sieve analysis of breakthrough HIV-1 sequences in HVTN 505 identifies vaccine pressure targeting the CD4 binding site of Env-gp120
#> 1907: An HIV-1 antibody from an elite neutralizer implicates the fusion peptide as a site of vulnerability
#> 1908: Complementary antibody lineages achieve neutralization breadth in an HIV-1 infected elite neutralizer
#> 1909: Identification of IOMA-class neutralizing antibodies targeting the CD4-binding site on the HIV-1 envelope glycoprotein
#> 1910: Nonparametric estimation of the causal effect of a stochastic threshold-based intervention
#> journal publication_date link pubmed_id related_studies studies_with_data
#> <char> <char> <char> <char> <char> <char>
#> 1: J Virol 2015 Feb https://www.ncbi.nlm.nih.gov/pubmed/25410856 25410856 <NA> <NA>
#> 2: Immunity 2018 Jan 16 https://www.ncbi.nlm.nih.gov/pubmed/29287996 29287996 <NA> <NA>
#> 3: NPJ Vaccines 2021 Oct 25 https://pubmed.ncbi.nlm.nih.gov/34697307 34697307 <NA> <NA>
#> 4: Viruses 2021 Oct 19 https://pubmed.ncbi.nlm.nih.gov/34696536 34696536 <NA> <NA>
#> 5: NPJ Digit Med 2025 May 06 https://pubmed.ncbi.nlm.nih.gov/40328984 40328984 <NA> <NA>
#> ---
#> 1906: PLOS ONE 2017 Nov 17 https://www.ncbi.nlm.nih.gov/pubmed/29149197 29149197 vtn505 vtn505
#> 1907: Nat Microbiol 2016 Nov 14 https://www.ncbi.nlm.nih.gov/pubmed/27841852 27841852 <NA> <NA>
#> 1908: PLoS Pathog 2022 Nov https://pubmed.ncbi.nlm.nih.gov/36395347 36395347 cvd850 <NA>
#> 1909: Nat Commun 2022 Aug 03 https://pubmed.ncbi.nlm.nih.gov/35922441 35922441 cvd850 <NA>
#> 1910: Biometrics 2023 Jun https://pubmed.ncbi.nlm.nih.gov/35526218 35526218 <NA> <NA>
#> publication_data_available
#> <lgcl>
#> 1: FALSE
#> 2: FALSE
#> 3: FALSE
#> 4: FALSE
#> 5: FALSE
#> ---
#> 1906: FALSE
#> 1907: FALSE
#> 1908: FALSE
#> 1909: FALSE
#> 1910: FALSEThis table summarizes all publications, providing some information
like first author, journal where it was published, and title as a
data.table. It also includes a pubmed url where available
under link. Related studies under
related_studies, and related studies with data available
under studies_with_data. We can use data.table
methods to filter and sort this table to browse available
publications.
For example, we can filter this table to view only publications related to a particular study:
vtn096_pubs <- con$availablePublications[grepl("vtn096", related_studies)]
vtn096_pubs
#> publication_id label first_author
#> <char> <char> <char>
#> 1: 1466 Cram 2019 (PLOS One) Data Cram JA
#> 2: 1921 <NA> Huang Y
#> 3: 250 <NA> Huang Y
#> 4: 267 <NA> Huang Y
#> 5: 268 <NA> Huang Y
#> 6: 1728 <NA> Mayer-Blackwell K
#> 7: 1392 Pantaleo 2019 (Lancet) Data Pantaleo G
#> 8: 1761 <NA> Seaton KE
#> 9: 1753 <NA> Stranix-Chibanda L
#> 10: 1420 <NA> Westling T
#> 11: 281 <NA> Yates NL
#> all_authors
#> <char>
#> 1: Cram JA, Fiore-Gartland AJ, Srinivasan S, Karuna S, Pantaleo G, Tomaras GD, Fredricks DN, Kublin JG
#> 2: Huang Y, Tarkhan A
#> 3: Huang Y, DiazGranados C, Janes H, Huang Y, deCamp A, Metch B, Grant S, Sanchez B, Phogat S, Koutsoukos M, Kanesa-Thasan N, Bourguignon P, Collard A, Buchbinder S, Tomaras GD, McElrath J, Gray G, Kublin J, Corey L, Gilbert PB
#> 4: Huang Y, Zhang L, Janes H, Frahm N, Isaacs A, Kim JH, Montefiori D, McElrath MJ, Tomaras GD, Gilbert PB
#> 5: Huang Y, Gilbert P, Fu R, Janes H
#> 6: Mayer-Blackwell K, Johnson AM, Potchen N, Minot SS, Heptinstall J, Seaton K, Sawant S, Shen X, Tomaras GD, Fiore-Gartland A, Kublin JG
#> 7: Pantaleo G, Janes H, Karuna S, Grant S, Ouedraogo GL, Allen M, Tomaras GD, Frahm N, Montefiori DC, Ferrari G, Ding S, Lee C, Robb ML, Esteban M, Wagner R, Bart PA, Rettby N, McElrath MJ, Gilbert PB, Kublin JG, Corey L, NIAID HIV Vaccine Trials Network
#> 8: Seaton KE, Deal A, Han X, Li SS, Clayton A, Heptinstall J, Duerr A, Allen MA, Shen X, Sawant S, Yates NL, Spearman P, Churchyard G, Goepfert PA, Maenza J, Gray G, Pantaleo G, Polakowski L, Robinson HL, Grant S, Randhawa AK, Huang Y, Morgan C, Grunenberg N, Karuna S, Gilbert PB, McElrath MJ, Huang Y, Tomaras GD, NIAID HIV Vaccine Trials Network (HVTN) 076, 088, 086, 096, 097, 205 Study Teams
#> 9: Stranix-Chibanda L, Yu C, Brewinski Isaacs M, Allen M, Andriesen J, Walsh SR
#> 10: Westling T, Juraska M, Seaton KE, Tomaras GD, Gilbert PB, Janes H
#> 11: Yates NL, deCamp AC, Korber BT, Liao HX, Irene C, Pinter A, Peacock J, Harris LJ, Sawant S, Hraber P, Shen X, Rerks-Ngarm S, Pitisuttithum P, Nitayapan S, Berman PW, Robb ML, Pantaleo G, Zolla-Pazner S, Haynes BF, Alam SM, Montefiori DC, Tomaras GD
#> title
#> <char>
#> 1: Human gut microbiota is associated with HIV-reactive immunoglobulin at baseline and following HIV vaccination
#> 2: Methods for feature selection in down-selection of vaccine regimens based on multivariate immune response endpoints
#> 3: Selection of HIV vaccine candidates for concurrent testing in an efficacy trial
#> 4: Predictors of durable immune responses six months after the last vaccination in preventive HIV vaccine trials
#> 5: Statistical methods for down-selection of treatment regimens based on multiple endpoints, with application to HIV vaccine trials
#> 6: Multi-trial analysis of HIV-1 envelope gp41-reactive antibodies among global recipients of candidate HIV-1 vaccines
#> 7: Safety and immunogenicity of a multivalent HIV vaccine comprising envelope protein with either DNA or NYVAC vectors (HVTN 096): a phase 1b, double-blind, placebo-controlled trial
#> 8: Meta-analysis of HIV-1 vaccine elicited mucosal antibodies in humans
#> 9: A retrospective analysis of incident pregnancy in Phase 1 and 2a HIV-1 vaccine study participants does not support concern for adverse pregnancy or birth outcomes
#> 10: Methods for comparing durability of immune responses between vaccine regimens in early-phase trials
#> 11: HIV-1 envelope glycoproteins from diverse clades differentiate antibody responses and durability among vaccinees
#> journal publication_date link pubmed_id
#> <char> <char> <char> <char>
#> 1: PLoS One 2019 https://www.ncbi.nlm.nih.gov/pubmed/31869338 31869338
#> 2: Stat Biosci 2020 https://pubmed.ncbi.nlm.nih.gov/32421096 32421096
#> 3: Curr Opin Virol 2016 Jan 28 http://www.ncbi.nlm.nih.gov/pubmed/26827165 26827165
#> 4: Vaccine 2017 Feb 22 https://www.ncbi.nlm.nih.gov/pubmed/28131393 28131393
#> 5: Biostatistics 2017 Apr 1 https://www.ncbi.nlm.nih.gov/pubmed/27649715 27649715
#> 6: Front Immunol 2022 https://pubmed.ncbi.nlm.nih.gov/36311720 36311720
#> 7: Lancet HIV 2019 Oct 7 https://www.ncbi.nlm.nih.gov/pubmed/31601541 31601541
#> 8: NPJ Vaccines 2021 Apr 15 https://pubmed.ncbi.nlm.nih.gov/33859204 33859204
#> 9: BMC Infect Dis 2021 Aug 11 https://pubmed.ncbi.nlm.nih.gov/34380464 34380464
#> 10: Stat Methods Med Res 2019 Jan 9 https://www.ncbi.nlm.nih.gov/pubmed/30623732 30623732
#> 11: J Virol 2018 Mar 28 https://www.ncbi.nlm.nih.gov/pubmed/29386288 29386288
#> related_studies
#> <char>
#> 1: vtn096
#> 2: mrv144, vtn096
#> 3: mrv144, vtn096
#> 4: mrv144, vtn096, vtn205
#> 5: mrv144, vtn096
#> 6: mrv144, vtn096, vtn097, vtn098, vtn100, vtn106, vtn107, vtn111, vtn122, vtn204, vtn205, vtn505
#> 7: mrv144, vtn096, vtn100
#> 8: vtn076, vtn086, vtn088, vtn096, vtn097, vtn205
#> 9: vtn026, vtn039, vtn040, vtn041, vtn042, vtn044, vtn045, vtn048, vtn049, vtn050, vtn052, vtn054, vtn055, vtn056, vtn057, vtn059, vtn060, vtn063, vtn064, vtn065, vtn067, vtn068, vtn069, vtn070, vtn071, vtn072, vtn073, vtn073E, vtn076, vtn077, vtn078, vtn080, vtn082, vtn083, vtn084, vtn085, vtn086, vtn087, vtn088, vtn090, vtn092, vtn094, vtn096, vtn097, vtn098, vtn100, vtn105, vtn106, vtn110, vtn111, vtn112, vtn203, vtn204, vtn205
#> 10: vtn094, vtn096
#> 11: mrv144, vtn096
#> studies_with_data publication_data_available
#> <char> <lgcl>
#> 1: <NA> TRUE
#> 2: <NA> FALSE
#> 3: <NA> FALSE
#> 4: <NA> FALSE
#> 5: <NA> FALSE
#> 6: vtn097, vtn505 FALSE
#> 7: <NA> TRUE
#> 8: vtn097 FALSE
#> 9: vtn097, vtn105 FALSE
#> 10: <NA> FALSE
#> 11: <NA> FALSEor publications that have related studies with integrated data in DataSpace:
pubs_with_study_data <- con$availablePublications[!is.na(studies_with_data)]
pubs_with_study_data |>
head()
#> publication_id label first_author
#> <char> <char> <char>
#> 1: 1540 Andersen-Nissen 2021 (PLOS Pathog) Data Andersen-Nissen E
#> 2: 213 <NA> Andrasik MP
#> 3: 218 <NA> Andrasik MP
#> 4: 225 <NA> Andrasik MP
#> 5: 226 <NA> Arnold MP
#> 6: 7 <NA> Asbach B
#> all_authors
#> <char>
#> 1: Andersen-Nissen E, Fiore-Gartland A, Ballweber Fleming L, Carpp LN, Naidoo AF, Harper MS, Voillet V, Grunenberg N, Laher F, Innes C, Bekker L-G, Kublin JG, Huang Y, Ferrari G, Tomaras GD, Gray G, Gilbert PB, McElrath MJ
#> 2: Andrasik MP, Yoon R, Mooney J, Broder G, Bolton M, Votto T, Davis-Vogel A; HVTN 505 study team; NIAID HIV Vaccine Trials Network
#> 3: Andrasik MP, Karuna ST, Nebergall M, Koblin BA, Kublin JG; NIAID HIV Vaccine Trials Network
#> 4: Andrasik MP, Chandler C, Powell B, Humes D, Wakefield S, Kripke K, Eckstein D
#> 5: Arnold MP, Andrasik M, Landers S, Karuna S, Mimiaga MJ, Wakefield S, Mayer K, Buchbinder S, Koblin BA
#> 6: Asbach B, Kliche A, Köstler J, Perdiguero B, Esteban M, Jacobs BL, Montefiori DC, LaBranche CC, Yates NL, Tomaras GD, Ferrari G, Foulds KE, Roederer M, Landucci G, Forthal DN, Seaman MS, Hawkins N, Self SG, Sato A, Gottardo R, Phogat S, Tartaglia J, Barnett SW, Burke B, Cristillo AD, Weiss DE, Francis J, Galmin L, Ding S, Heeney JL, Pantaleo G, Wagner R
#> title
#> <char>
#> 1: Innate immune signatures to a partially-efficacious HIV vaccine predict correlates of HIV-1 infection risk
#> 2: Exploring barriers and facilitators to participation of male-to-female transgender persons in preventive HIV vaccine clinical trials.
#> 3: Behavioral risk assessment in HIV Vaccine Trials Network (HVTN) clinical trials: A qualitative study exploring HVTN staff perspectives
#> 4: Bridging the divide: HIV prevention research and Black men who have sex with men
#> 5: Sources of racial/ethnic differences in HIV vaccine trial awareness: Exposure, attention, or both?
#> 6: Potential to streamline heterologous DNA prime and NYVAC/protein boost HIV vaccine regimens in rhesus macaques by employing improved antigens
#> journal publication_date link pubmed_id
#> <char> <char> <char> <char>
#> 1: PLOS Pathog 2021 <NA> 33720973
#> 2: Prev Sci 2014 Jun http://www.ncbi.nlm.nih.gov/pubmed/23446435 23446435
#> 3: Vaccine 2013 Sep 13 http://www.ncbi.nlm.nih.gov/pubmed/23859840 23859840
#> 4: Am J Public Health 2014 Apr http://www.ncbi.nlm.nih.gov/pubmed/24524520 24524520
#> 5: Am J Public Health 2014 Aug http://www.ncbi.nlm.nih.gov/pubmed/24922153 24922153
#> 6: J Virol 2016 Mar 28 http://www.ncbi.nlm.nih.gov/pubmed/26865719 26865719
#> related_studies studies_with_data publication_data_available
#> <char> <char> <lgcl>
#> 1: vtn097 vtn097 TRUE
#> 2: vtn505 vtn505 FALSE
#> 3: vtn069, vtn404, vtn502, vtn503, vtn504, vtn505, vtn802, vtn903, vtn906, vtn907 vtn505 FALSE
#> 4: vtn505 vtn505 FALSE
#> 5: vtn505 vtn505 FALSE
#> 6: cvd277, cvd281 cvd277, cvd281 FALSEWe can also use this information to connect to related studies and pull integrated data. Say we are interested in this Rouphael (2019) publication:
rouphael2019 <- con$availablePublications[first_author == "Rouphael NG"]
rouphael2019
#> publication_id label first_author
#> <char> <char> <char>
#> 1: 1390 Rouphael 2019 (J Clin Invest) Data Rouphael NG
#> 2: 1887 <NA> Rouphael NG
#> all_authors
#> <char>
#> 1: Rouphael NG, Morgan C, Li SS, Jensen R, Sanchez B, Karuna S, Swann E, Sobieszczyk ME, Frank I, Wilson GJ, Tieu HV, Maenza J, Norwood A, Kobie J, Sinangil F, Pantaleo G, Ding S, McElrath MJ, De Rosa SC, Montefiori DC, Ferrari G, Tomaras GD, Keefer MC, HVTN 105 Protocol Team and the NIAID HIV Vaccine Trials Network
#> 2: Rouphael NG, Branche AR, Diemert DJ, Falsey AR, Losada C, Baden LR,Frey SE, Whitaker JA, Little SJ, Kamidani S, Walter EB, Novak RM, Rupp R, Jackson LA, Babu TM, Kottkamp AC, Luetkemeyer AF, Immergluck LC, Presti RM, Bäcker M, Winokur PL, Mahgoub SM, Goepfert PA, Fusco DN, Atmar RL, Posavad CM, Netzl A, Smith DJ, Telu K, Mu J, McQuarrie LJ, Makowski M, Makhene MK, Crandon S, Montefiori DC, Roberts PC, Beigel JH; Coronavirus Variant Immunologic Landscape Trial (COVAIL) Study Team
#> title
#> <char>
#> 1: DNA priming and gp120 boosting induces HIV-specific antibodies in a randomized clinical trial
#> 2: Immunogenicity of a 2-dose regimen of Moderna mRNA beta/omicron BA.1 bivalent variant vaccine boost in a randomized clinical trial
#> journal publication_date link pubmed_id related_studies studies_with_data
#> <char> <char> <char> <char> <char> <char>
#> 1: J Clin Invest 2019 Sep 30 https://www.ncbi.nlm.nih.gov/pubmed/31566579 31566579 vtn105 vtn105
#> 2: J Infect Dis 2023 Dec 20 https://pubmed.ncbi.nlm.nih.gov/37561027 37561027 <NA> <NA>
#> publication_data_available
#> <lgcl>
#> 1: TRUE
#> 2: FALSEWe can find this publication in the available publications table, determine related studies, and pull data for those studies where available.
## note here we are passing the column `related_studies` here where in
## this case has a single study_id. Other entries are comma separated
## and need to be split, for example:
## `con$availablePublications[,strsplit(related_studies, ", ") |> unlist() |> unique()]`
rouphael2019_study <- rouphael2019$related_studies |>
con$getStudies()
rouphael2019_study
#> <DataSpaceStudies>
#> Studies: vtn105
#> Available integrated datasets:
#> - Binding Ab multiplex assay
#> - Demographics
#> - Intracellular Cytokine Staining
#> - Neutralizing antibody
#> Available non-integrated datasets:
#> Available publication datasets:
#> - Rouphael 2019 (J Clin Invest) Data
#> Available Studies objects:
#> - availableDatasets
#> - datasets
#> - studies
#> - studyInfo
#> - treatmentArm
#> - variableDefinitions
#> Available Studies methods:
#> - loadAvailableDatasets
#> Available Connection objects:
#> - availableDonors
#> - availableGroups
#> - availableMabMixtures
#> - availableMabs
#> - availablePublications
#> - availableStudies
#> - availableViruses
#> - virusNameMappingTables
#> Available Connection methods:
#> - downloadPublicationData
#> - getDaash
#> - getDonors
#> - getGroups
#> - getMabs
#> - getStudies
rouphael2019_study$availableDatasets
#> study_id dataset_type assay_identifier assay_label
#> <char> <char> <char> <char>
#> 1: vtn105 Integrated Assay BAMA Binding Ab multiplex assay
#> 2: vtn105 Integrated Assay Demographics Demographics
#> 3: vtn105 Integrated Assay ICS Intracellular Cytokine Staining
#> 4: vtn105 Integrated Assay NAb Neutralizing antibodyWe can see that there are datasets available for this study. We can
pull any of them using rouphael2019_study$getDataset().
DataSpace also includes publication datasets for some publications.
The format of this data will vary from publication to publication, and
is stored in a zip file. The publication_data_available
field specifies publications where publication data is available.
Data for a publication can be accessed through by either passing a
publication_id value or an
availablePublications object to the
downloadPublicationData connection method.
Here, we download data for publication with ID 1461 (Westling, 2020),
and view the resulting downloads. Like the get... methods,
you may pass the availablePublications object to download
publication data listed in that table.
publicationDataFiles <- con$availablePublications[label %like% "Westling 2020"] |>
con$downloadPublicationData()
basename(publicationDataFiles)
#> [1] "Westling1461_publicationData.zip"All zip files will include a file format document as a PDF, as well
as a README. These documents will give an overview of the remaining
contents of the files. In this case, data is separated by CD8+ T-cell
responses and CD4+ T-cell responses, as described in the
README.txt.