The HGNCREST package provides functions for querying the HGNC REST
API. The functions follow the HUGO Gene Nomenclature Committee (HGNC)
REST API documentation at https://www.genenames.org/help/rest/. There
are three main operations that can be performed with this package:
- fetching general information about the HGNC database (
hgnc_info). - fetching information about a specific gene (
hgnc_fetch) - searching for genes based on a query (
hgnc_search)
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("waldronlab/HGNCREST")library(HGNCREST)The hgnc_info function returns general information about the HGNC
database. It includes searchableFields and storedFields metadata.
hgnc_info()
#> $lastModified
#> [1] "2024-11-12T13:14:30.758Z"
#>
#> $numDoc
#> [1] 45613
#>
#> $responseHeader
#> $responseHeader$QTime
#> [1] 0
#>
#> $responseHeader$status
#> [1] 0
#>
#>
#> $searchableFields
#> [1] "refseq_accession" "mgd_id" "locus_group" "vega_id" "uniprot_ids"
#> [6] "ensembl_gene_id" "alias_symbol" "curator_notes" "hgnc_id" "omim_id"
#> [11] "ucsc_id" "rna_central_id" "name" "ena" "prev_symbol"
#> [16] "ccds_id" "locus_type" "alias_name" "mane_select" "rgd_id"
#> [21] "location" "symbol" "entrez_id" "status" "prev_name"
#>
#> $storedFields
#> [1] "snornabase" "mirbase" "prev_name"
#> [4] "enzyme_id" "uuid" "pubmed_id"
#> [7] "prev_name" "agr" "lsdb"
#> [10] "ccds_id" "ena" "locus_type"
#> [13] "bioparadigms_slc" "rna_central_id" "date_symbol_changed"
#> [16] "cd" "alias_name" "mamit-trnadb"
#> [19] "alias_symbol" "location" "gencc"
#> [22] "uniprot_ids" "mgd_id" "date_name_changed"
#> [25] "entrez_id" "status" "orphanet"
#> [28] "location" "symbol" "date_approved_reserved"
#> [31] "lncrnadb" "gtrnadb" "_version_"
#> [34] "prev_symbol" "pseudogene.org" "homeodb"
#> [37] "alias_name" "mane_select" "rgd_id"
#> [40] "horde_id" "ucsc_id" "omim_id"
#> [43] "name" "merops" "lncipedia"
#> [46] "imgt" "iuphar" "date_modified"
#> [49] "cosmic" "hgnc_id" "curator_notes"
#> [52] "gene_group_id" "vega_id" "ensembl_gene_id"
#> [55] "refseq_accession" "locus_group" "gene_group"The searchableFields function is a convenience function that returns a
character vector of searchable fields in the HGNC database.
searchableFields()
#> [1] "alias_symbol" "curator_notes" "hgnc_id" "uniprot_ids" "vega_id"
#> [6] "ensembl_gene_id" "refseq_accession" "mgd_id" "locus_group" "entrez_id"
#> [11] "prev_name" "status" "symbol" "location" "locus_type"
#> [16] "prev_symbol" "ccds_id" "ena" "mane_select" "rgd_id"
#> [21] "alias_name" "omim_id" "ucsc_id" "name" "rna_central_id"The hgnc_fetch function returns a tibble with information about the
gene specified by the searchableField and value arguments.
hgnc_fetch("ena", "BC040926")
#> # A tibble: 3 × 26
#> date_modified date_approved_reserved locus_group gene_group_id uuid locus_type agr
#> <chr> <chr> <chr> <int> <chr> <chr> <chr>
#> 1 2013-06-27T00:00:00Z 2009-07-20T00:00:00Z non-coding RNA 1987 2d9067ca-… RNA, long… HGNC…
#> 2 2013-06-27T00:00:00Z 2009-07-20T00:00:00Z non-coding RNA 1987 2d9067ca-… RNA, long… HGNC…
#> 3 2013-06-27T00:00:00Z 2009-07-20T00:00:00Z non-coding RNA 1987 2d9067ca-… RNA, long… HGNC…
#> # ℹ 19 more variables: date_name_changed <chr>, ensembl_gene_id <chr>, symbol <chr>, entrez_id <chr>,
#> # prev_name <chr>, prev_symbol <chr>, ucsc_id <chr>, name <chr>, ena <chr>, rna_central_id <chr>,
#> # status <chr>, date_symbol_changed <chr>, hgnc_id <chr>, vega_id <chr>, refseq_accession <chr>,
#> # lncipedia <chr>, alias_symbol <chr>, location <chr>, gene_group <chr>The hgnc_search function searches for genes based on a query. It
returns a data.frame with information about the genes that match the
query.
hgnc_search("symbol", "BRCA1")
#> symbol hgnc_id score
#> 1 BRCA1 HGNC:1100 4.692048The hgnc_search function also allows for more complex queries using
the query argument. The query should be a string that follows the HGNC
REST API query syntax.
hgnc_search("symbol", c("ZNF*", "AND", "status:Approved")) |>
head()
#> symbol hgnc_id score
#> 1 ZNF2 HGNC:12991 1.018264
#> 2 ZNF3 HGNC:13089 1.018264
#> 3 ZNF7 HGNC:13139 1.018264
#> 4 ZNF8 HGNC:13154 1.018264
#> 5 ZNF8-DT HGNC:55280 1.018264
#> 6 ZNF8-ERVK3-1 HGNC:56757 1.018264In this example, we search for genes with the name “MAPK interacting” and that have a locus type of “gene with protein product”. Note that “locus_type” is a searchable field in the HGNC database that can be used to filter the search results.
hgnc_search(
"name",
c("MAPK interacting", "AND", "locus_type:gene with protein product")
)
#> symbol hgnc_id score
#> 1 MKNK1 HGNC:7110 8.759536
#> 2 MKNK2 HGNC:7111 8.759536The HGNCREST package provides a convenient way to query the HGNC REST
API from R. It allows users to fetch information about specific genes,
search for genes based on a query, and get general information about the
HGNC database.
Click to expand
sessionInfo()
#> R Under development (unstable) (2024-11-03 r87286)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.1 LTS
#>
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#> BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
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#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
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#>
#> time zone: America/New_York
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] HGNCREST_0.99.0 httr2_1.0.6
#>
#> loaded via a namespace (and not attached):
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#> [21] shiny_1.9.1 rlang_1.1.4 ellipsis_0.3.2 remotes_2.5.0
#> [25] withr_3.0.2 cachem_1.1.0 yaml_2.3.10 devtools_2.4.5
#> [29] BiocBaseUtils_1.9.0 tools_4.5.0 memoise_2.0.1 dplyr_1.1.4
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#> [37] R6_2.5.1 mime_0.12 lifecycle_1.0.4 fs_1.6.5
#> [41] htmlwidgets_1.6.4 usethis_3.0.0 miniUI_0.1.1.1 pkgconfig_2.0.3
#> [45] desc_1.4.3 pillar_1.9.0 later_1.3.2 glue_1.8.0
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#> [53] tibble_3.2.1 tidyselect_1.2.1 sys_3.4.3 rstudioapi_0.17.1
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