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Display OGRDB citation information
Display OGRDB citation information when selecting OGRDB germline db and in man pages for download_OGRDB_germline_sequences() and download_OGRDB_germline_json().
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Lines changed: 67 additions & 42 deletions

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‎R/use_germline_db.R‎

Lines changed: 30 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -34,23 +34,37 @@
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c(wmsg(msg1), "\n ", wmsg(msg2))
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}
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37-
.note_on_selecting_AIRR_src_germline_db <- function(db_name)
37+
.notes_on_selecting_OGRDB_germline_db <- function(db_name)
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{
39-
is_src_db <- (has_prefix(db_name, "_AIRR.") ||
40-
has_prefix(db_name, "_OGRDB.")) && has_suffix(db_name, ".src")
41-
if (!is_src_db)
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is_ogrdb_db <- has_prefix(db_name, "_AIRR.") ||
40+
has_prefix(db_name, "_OGRDB.")
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if (!is_ogrdb_db)
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return()
43-
ref_db_name <- sub("\\.src$", "", db_name)
44-
url <- "https://ogrdb.airr-community.org/germline_set/75"
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msg1 <- c("Use ", db_name, " only if you know what you are doing.")
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msg2 <- c("Note that the allele sequences in ", db_name, " come from ",
47-
"the \"Source Set\" datasets provided by AIRR-community/OGRDB. ",
48-
"However, the AIRR-community/OGRDB maintainers recommend ",
49-
"using the allele sequences from the \"Reference Set\" ",
50-
"datasets for AIRR-seq analysis (see for example ", url, "), ",
51-
"which are provided by ", ref_db_name, ".")
52-
message(" ", wmsg(msg1), "\n\n ", wmsg(msg2), "\n\n ",
53-
.how_to_suppress_use_germline_db_msg(db_name))
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msg1 <- "If you use OGRDB in your research, please cite:"
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msg2 <- c("The current landscape of adaptive immune receptor ",
45+
"genomic and repertoire data: OGRDB and VDJbase")
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msg3 <- c("Lees, Peres, Klein, Amos et al., Nucleic Acids Research, ",
47+
"November 2025.")
48+
msg4 <- "https://doi.org/10.1093/nar/gkaf1094"
49+
message(" ", wmsg(msg1),
50+
"\n\n ", wmsg(msg2, margin=4),
51+
"\n ", wmsg(msg3, margin=4),
52+
"\n ", wmsg(msg4, margin=4))
53+
is_src_db <- has_suffix(db_name, ".src")
54+
if (is_src_db) {
55+
ref_db_name <- sub("\\.src$", "", db_name)
56+
url <- "https://ogrdb.airr-community.org/germline_set/75"
57+
msg1 <- c("Use ", db_name, " only if you know what you are doing.")
58+
msg2 <- c("Note that the allele sequences in ", db_name, " come ",
59+
"from the \"Source Set\" datasets provided by OGRDB. ",
60+
"However, the AIRR-community/OGRDB maintainers ",
61+
"recommend using the allele sequences from the ",
62+
"\"Reference Set\" datasets for AIRR-seq analysis ",
63+
"(see for example ", url, "), which are provided ",
64+
"by ", ref_db_name, ".")
65+
message("\n ", wmsg(msg1), "\n\n ", wmsg(msg2))
66+
}
67+
message("\n ", .how_to_suppress_use_germline_db_msg(db_name))
5468
}
5569

5670
.note_on_selecting_IMGT_germline_db <- function(db_name)
@@ -68,7 +82,7 @@
6882
if (has_prefix(db_name, "_AIRR.")) {
6983
warn_if_old_AIRR_dbs_are_present()
7084
} else {
71-
.note_on_selecting_AIRR_src_germline_db(db_name)
85+
.notes_on_selecting_OGRDB_germline_db(db_name)
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.note_on_selecting_IMGT_germline_db(db_name)
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}
7488

‎man/download_IMGT_germline_sequences.Rd‎

Lines changed: 7 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,8 @@
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The \code{download_IMGT_germline_sequences()} function downloads
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germline V/D/J gene allele sequences (nucleotides) from the IMGT/V-QUEST
1313
download site for a given IMGT/V-QUEST release and organism.
14-
The sequences are downloaded in several FASTA files, one per "IMGT group".
14+
The sequences are downloaded in several FASTA files, one per
15+
\emph{IMGT group}.
1516

1617
CONDITIONS OF USE AND LICENSE: The IMGT data is provided to the academic
1718
users and NPO's (Not for Profit Organization(s)) under the CC BY-NC-ND 4.0
@@ -66,11 +67,12 @@ IMGT_is_up()
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Note that:
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\itemize{
6869
\item The names of the downloaded files follow the <IMGT group>.fasta
69-
convention, where <IMGT group> is one of the 7 "IG" groups or
70-
10 "TR" groups.
70+
convention, where <IMGT group> is one of the 7 \emph{IMGT groups}
71+
with the "IG" prefix or one of the 10 \emph{IMGT groups} with
72+
the "TR" prefix.
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\item IMGT doesn't always provide germline sequences for
72-
all IMGT groups. This means that, depending on the IMGT/V-QUEST
73-
release and organism, some FASTA files can be missing.
74+
all \emph{IMGT groups}. This means that, depending on the
75+
IMGT/V-QUEST release and organism, some FASTA files can be missing.
7476
}
7577
}
7678
\item{destdir}{

‎man/download_OGRDB_germline_json.Rd‎

Lines changed: 7 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -14,6 +14,12 @@
1414
allele FWR/CDR annotations (a.k.a. V gene delineations) from
1515
an OGRDB JSON file. Note that it's a simple reimplementation in R
1616
of the Python script \code{makeogrannote.py} included in IgBLAST.
17+
18+
If you use OGRDB in your research, please cite:
19+
\preformatted{ The current landscape of adaptive immune receptor genomic and
20+
repertoire data: OGRDB and VDJbase
21+
Lees, Peres, Klein, Amos et al., Nucleic Acids Research, November 2025.
22+
https://doi.org/10.1093/nar/gkaf1094}
1723
}
1824
1925
\usage{
@@ -96,12 +102,7 @@ makeogrannote(ogrdb_json_file)
96102
\item \link{intdata_utils} to access and manipulate IgBLAST
97103
\emph{internal data}.
98104

99-
\item The \code{\link{igblastn}} function to run the \code{igblastn}
100-
\emph{standalone executable} included in IgBLAST from R. This
101-
is the main function in the \pkg{igblastr} package.
102-
103-
\item IgBLAST is described at
104-
\url{https://pubmed.ncbi.nlm.nih.gov/23671333/}.
105+
\item The OGRDB website: \url{https://ogrdb.airr-community.org/}.
105106
}
106107
}
107108

‎man/download_OGRDB_germline_sequences.Rd‎

Lines changed: 23 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,14 @@
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The \code{download_OGRDB_germline_sequences()} function downloads
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germline V/D/J gene allele sequences (nucleotides) from OGRDB for
1010
the specified germline sets.
11-
The sequences are downloaded in several FASTA files, one per "IMGT group".
11+
The sequences are downloaded in several FASTA files, one per
12+
\emph{IMGT group}.
13+
14+
If you use OGRDB in your research, please cite:
15+
\preformatted{ The current landscape of adaptive immune receptor genomic and
16+
repertoire data: OGRDB and VDJbase
17+
Lees, Peres, Klein, Amos et al., Nucleic Acids Research, November 2025.
18+
https://doi.org/10.1093/nar/gkaf1094}
1219
}
1320

1421
\usage{
@@ -33,25 +40,26 @@ download_OGRDB_germline_sequences(organism, germline_sets,
3340
Species, and click on "Show Germline Sets" to see the list of germline
3441
sets available for that species and their versions.
3542

36-
Note that each OGRDB germline set corresponds to one or more "IMGT groups",
37-
where an "IMGT group" is a combination of locus and region type. For
38-
example:
43+
Note that each OGRDB germline set corresponds to one or more
44+
\emph{IMGT groups}, where an \emph{IMGT group} is a combination
45+
of locus and region type. For example:
3946
\itemize{
40-
\item Germline set \code{IGH_VDJ} corresponds to IMGT groups IGHV,
41-
IGHD, and IGHJ.
42-
\item Germline set \code{IGLambda_VJ} corresponds to IMGT groups IGLV
43-
and IGLJ.
44-
\item Germline set \code{PWD/PhJ IGH} corresponds to IMGT groups IGHV,
45-
IGHD, and IGHJ.
46-
\item Germline set \code{PWD/PhJ IGKV} corresponds to IMGT group IGKV.
47+
\item Germline set \code{IGH_VDJ} corresponds to \emph{IMGT groups}
48+
IGHV, IGHD, and IGHJ.
49+
\item Germline set \code{IGLambda_VJ} corresponds to \emph{IMGT groups}
50+
IGLV and IGLJ.
51+
\item Germline set \code{PWD/PhJ IGH} corresponds to \emph{IMGT groups}
52+
IGHV, IGHD, and IGHJ.
53+
\item Germline set \code{PWD/PhJ IGKV} corresponds to \emph{IMGT group}
54+
IGKV.
4755
}
48-
For reference, the 10 "IMGT groups" for B-cell Receptors are:
56+
For reference, the 10 \emph{IMGT groups} for B-cell Receptors are:
4957
\preformatted{ IGHV, IGHD, IGHJ, IGHC,
5058
IGKV, IGKJ, IGKC,
5159
IGLV, IGLJ, IGLC}
5260

5361
IMPORTANT: The germline sets in your \code{germline_sets} vector must
54-
correspond to distinct IMGT groups.
62+
correspond to distinct \emph{IMGT groups}.
5563

5664
Here is an example of valid \code{germline_sets} vector for Mus musculus:
5765
\preformatted{ germline_sets <- c(`PWD/PhJ IGH`=2,
@@ -141,7 +149,7 @@ download_OGRDB_germline_sequences("Macaca mulatta", germline_sets,
141149
destdir=destdir)
142150
143151
## List the downloaded files:
144-
list.files(destdir) # 7 FASTA files
152+
list.files(destdir) # 7 FASTA files (one per IMGT group)
145153
146154
## Remove temporary directory:
147155
unlink(destdir, recursive=TRUE)
@@ -163,7 +171,7 @@ download_OGRDB_germline_sequences("Mus musculus", germline_sets,
163171
destdir=destdir)
164172
165173
## List the downloaded files:
166-
list.files(destdir) # 7 FASTA files
174+
list.files(destdir) # 7 FASTA files (one per IMGT group)
167175
168176
## Remove temporary directory:
169177
unlink(destdir, recursive=TRUE)

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