Getting PGS Publications

PGS Publications

PGS publications are those published works that underlie the data provided by the PGS Catalog.

To retrieve these publications use the function get_publications(). You may use one of the following search criteria (or a combination thereof):

pgp_id: the publication identifier assigned by the PGS Catalog;
pgs_id: the polygenic score identifier;
pubmed_id: PubMed identifier;
author: an author last name.

If you do not pass any of the criteria above, then get_publications() will retrieve all publications in the Catalog.

Getting PGS publications by their identifiers:

library(quincunx)

get_publications(pgp_id = c('PGP000001', 'PGP000002'))
#> An object of class "publications"
#> Slot "publications":
#> # A tibble: 2 × 8
#>   pgp_id    pubmed_id publication_date publication   title author_fullname doi  
#>   <chr>         <int> <date>           <chr>         <chr> <chr>           <chr>
#> 1 PGP000001  25855707 2015-04-08       J Natl Cance… Pred… Mavaddat N      10.1…
#> 2 PGP000002  30554720 2018-12-13       Am J Hum Gen… Poly… Mavaddat N      10.1…
#> # ℹ 1 more variable: authors <chr>
#> 
#> Slot "pgs_ids":
#> # A tibble: 21 × 3
#>    pgp_id    pgs_id    stage   
#>    <chr>     <chr>     <chr>   
#>  1 PGP000001 PGS000001 gwas/dev
#>  2 PGP000001 PGS000002 gwas/dev
#>  3 PGP000001 PGS000003 gwas/dev
#>  4 PGP000001 PGS000001 eval    
#>  5 PGP000001 PGS000002 eval    
#>  6 PGP000001 PGS000003 eval    
#>  7 PGP000002 PGS000004 gwas/dev
#>  8 PGP000002 PGS000005 gwas/dev
#>  9 PGP000002 PGS000006 gwas/dev
#> 10 PGP000002 PGS000007 gwas/dev
#> # ℹ 11 more rows

By pgs_id:

get_publications(pgs_id = 'PGS000003')
#> An object of class "publications"
#> Slot "publications":
#> # A tibble: 1 × 8
#>   pgp_id    pubmed_id publication_date publication   title author_fullname doi  
#>   <chr>         <int> <date>           <chr>         <chr> <chr>           <chr>
#> 1 PGP000001  25855707 2015-04-08       J Natl Cance… Pred… Mavaddat N      10.1…
#> # ℹ 1 more variable: authors <chr>
#> 
#> Slot "pgs_ids":
#> # A tibble: 6 × 3
#>   pgp_id    pgs_id    stage   
#>   <chr>     <chr>     <chr>   
#> 1 PGP000001 PGS000001 gwas/dev
#> 2 PGP000001 PGS000002 gwas/dev
#> 3 PGP000001 PGS000003 gwas/dev
#> 4 PGP000001 PGS000001 eval    
#> 5 PGP000001 PGS000002 eval    
#> 6 PGP000001 PGS000003 eval

By pubmed_id:

get_publications(pubmed_id = '30554720')
#> An object of class "publications"
#> Slot "publications":
#> # A tibble: 1 × 8
#>   pgp_id    pubmed_id publication_date publication   title author_fullname doi  
#>   <chr>         <int> <date>           <chr>         <chr> <chr>           <chr>
#> 1 PGP000002  30554720 2018-12-13       Am J Hum Gen… Poly… Mavaddat N      10.1…
#> # ℹ 1 more variable: authors <chr>
#> 
#> Slot "pgs_ids":
#> # A tibble: 15 × 3
#>    pgp_id    pgs_id    stage   
#>    <chr>     <chr>     <chr>   
#>  1 PGP000002 PGS000004 gwas/dev
#>  2 PGP000002 PGS000005 gwas/dev
#>  3 PGP000002 PGS000006 gwas/dev
#>  4 PGP000002 PGS000007 gwas/dev
#>  5 PGP000002 PGS000008 gwas/dev
#>  6 PGP000002 PGS000009 gwas/dev
#>  7 PGP000002 PGS000001 eval    
#>  8 PGP000002 PGS000002 eval    
#>  9 PGP000002 PGS000003 eval    
#> 10 PGP000002 PGS000004 eval    
#> 11 PGP000002 PGS000005 eval    
#> 12 PGP000002 PGS000006 eval    
#> 13 PGP000002 PGS000007 eval    
#> 14 PGP000002 PGS000008 eval    
#> 15 PGP000002 PGS000009 eval

By author:

get_publications(author = 'Natarajan')
#> An object of class "publications"
#> Slot "publications":
#> # A tibble: 23 × 8
#>    pgp_id    pubmed_id publication_date publication  title author_fullname doi  
#>    <chr>         <int> <date>           <chr>        <chr> <chr>           <chr>
#>  1 PGP000006  30104762 2018-08-13       Nat Genet    Geno… Khera AV        10.1…
#>  2 PGP000030  31676865 2019-11-01       Nat Genet    Geno… Klarin D        10.1…
#>  3 PGP000042  28223407 2017-02-21       Circulation  Poly… Natarajan P     10.1…
#>  4 PGP000060  30586733 2019-03-01       Circulation  Whol… Khera AV        10.1…
#>  5 PGP000076  27959714 2016-11-13       N Engl J Med Gene… Khera AV        10.1…
#>  6 PGP000116  32498804 2020-06-01       J Am Coll C… Limi… Aragam KG       10.1…
#>  7 PGP000127  33021622 2020-10-06       JAMA Cardiol Clin… Trinder M       10.1…
#>  8 PGP000159  32981348 2020-09-28       Circulation  Gene… Klarin D        10.1…
#>  9 PGP000230  34887591 2021-12-09       Nature       The … Graham SE       http…
#> 10 PGP000252  33433237 2021-01-12       Circ Genom … Inte… Ye Y            10.1…
#> # ℹ 13 more rows
#> # ℹ 1 more variable: authors <chr>
#> 
#> Slot "pgs_ids":
#> # A tibble: 461 × 3
#>    pgp_id    pgs_id    stage   
#>    <chr>     <chr>     <chr>   
#>  1 PGP000006 PGS000013 gwas/dev
#>  2 PGP000006 PGS000014 gwas/dev
#>  3 PGP000006 PGS000015 gwas/dev
#>  4 PGP000006 PGS000016 gwas/dev
#>  5 PGP000006 PGS000017 gwas/dev
#>  6 PGP000006 PGS000013 eval    
#>  7 PGP000006 PGS000014 eval    
#>  8 PGP000006 PGS000015 eval    
#>  9 PGP000006 PGS000016 eval    
#> 10 PGP000006 PGS000017 eval    
#> # ℹ 451 more rows

Getting PGS Publications by other criteria

The PGS Catalog REST API only supports searches by those criteria mentioned above. If you would like to get results by other criteria, e.g., publication_date, then you need to retrieve all publications and filter them afterwards.

As an example, let’s download all publications and then keep only those publications published in 2021:

all_pub <- get_publications(interactive = FALSE)
all_pub@publications
#> # A tibble: 708 × 8
#>    pgp_id    pubmed_id publication_date publication  title author_fullname doi  
#>    <chr>         <int> <date>           <chr>        <chr> <chr>           <chr>
#>  1 PGP000001  25855707 2015-04-08       J Natl Canc… Pred… Mavaddat N      10.1…
#>  2 PGP000002  30554720 2018-12-13       Am J Hum Ge… Poly… Mavaddat N      10.1…
#>  3 PGP000003  25748612 2015-03-04       Lancet       Gene… Mega JL         10.1…
#>  4 PGP000004  26392438 2015-09-20       Eur Heart J  Risk… Tada H          10.1…
#>  5 PGP000005  27655226 2016-09-21       Eur Heart J  Geno… Abraham G       10.1…
#>  6 PGP000006  30104762 2018-08-13       Nat Genet    Geno… Khera AV        10.1…
#>  7 PGP000007  30309464 2018-10-01       J Am Coll C… Geno… Inouye M        10.1…
#>  8 PGP000008  31184202 2019-06-11       Circ Genom … Vali… Wünnemann F     10.1…
#>  9 PGP000009  28456682 2017-04-06       J Clin Lipi… Poly… Paquette M      10.1…
#> 10 PGP000010  27513194 2016-08-11       Genet Med    Pers… Läll K          10.1…
#> # ℹ 698 more rows
#> # ℹ 1 more variable: authors <chr>

Filtering based on the year 2021:

library(dplyr, warn.conflicts = FALSE)

# Determine the PGP ids whose publication date falls within 2021.
pgp_ids_2021 <-
  filter(
    all_pub@publications,
    publication_date >= '2021-01-01' &
      publication_date <= '2021-12-31'
  ) |>
  pull('pgp_id')

# Filtering based on the PGP ids
pub_2021 <- all_pub[pgp_ids_2021]

# Print the first 10 PGS publications
pub_2021@publications
#> # A tibble: 97 × 8
#>    pgp_id    pubmed_id publication_date publication title  author_fullname doi  
#>    <chr>         <int> <date>           <chr>       <chr>  <chr>           <chr>
#>  1 PGP000050  33579919 2021-02-12       Nat Commun  Cross… Graff RE        10.1…
#>  2 PGP000058  33623038 2021-02-23       Nat Commun  Polyg… Huynh-Le MP     10.1…
#>  3 PGP000121  33608049 2021-02-19       Genome Med  Devel… Tam CHT         10.1…
#>  4 PGP000122  33398198 2021-01-04       Nat Genet   Trans… Conti DV        10.1…
#>  5 PGP000128  33462484 2021-01-18       Nat Genet   Genet… Sinnott-Armstr… 10.1…
#>  6 PGP000137  34750571 2021-11-08       Nat Metab   Integ… Ritchie SC      10.1…
#>  7 PGP000138  33420020 2021-01-08       Nat Commun  Disea… Fontanillas P   10.1…
#>  8 PGP000146  33495597 2021-01-25       Nat Genet   Commo… Harper AR       10.1…
#>  9 PGP000147  33623009 2021-02-23       Nat Commun  Whole… Thareja G       10.1…
#> 10 PGP000148  33472890 2021-01-20       Cancer Res  Asses… Hung RJ         10.1…
#> # ℹ 87 more rows
#> # ℹ 1 more variable: authors <chr>