Functions for querying the VGNC REST sister API
VGNCREST.RdThe functions follow the VGNC REST API documentation at
https://www.genenames.org/help/rest/. There are three main operations
that can be performed with this package: fetching information about a
specific gene (vgnc_fetch), searching for genes based on a query
(vgnc_search), and fetching general information about the VGNC database
(vgnc_info).
Arguments
- searchableField
character(1)A field as provided bysearchableFields().- value
character(1)A value to search for in thesearchableField.- query
character()A query string to search for in the HGNC database. The query string can be a single string or a vector of strings. If the query is a vector, the strings are concatenated with a "+". The query string can contain logical operators such as "AND", "OR", and "NOT". The query string can also contain field-value pairs separated by a colon. For example, to search for genes with the symbol starting with "ZNF" and the status "Approved", the query string would be c("ZNF*", "AND", "status:Approved").
Value
vgnc_info: A list of general information about the VGNC database. It
includes searchableFields and storedFields metadata.
vgnc_fetch: A tibble with information about the gene specified by
the searchableField and value arguments.
vgnc_search: A data.frame with information about the genes that
match the query in the searchableField.
Examples
vgnc_info()
#> $lastModified
#> [1] "2025-05-06T13:38:21.968Z"
#>
#> $numDoc
#> [1] 45901
#>
#> $responseHeader
#> $responseHeader$QTime
#> [1] 1
#>
#> $responseHeader$status
#> [1] 0
#>
#>
#> $searchableFields
#> [1] "name" "status" "alias_symbol"
#> [4] "ccds_id" "rna_central_id" "alias_name"
#> [7] "refseq_accession" "locus_type" "prev_name"
#> [10] "omim_id" "alias_name_string" "mgd_id"
#> [13] "symbol" "mane_select" "rgd_id"
#> [16] "entrez_id" "uniprot_ids" "hgnc_id"
#> [19] "locus_group" "location_sortable" "prev_symbol"
#> [22] "curator_notes" "ena" "ensembl_gene_id"
#> [25] "vega_id" "ucsc_id" "prev_name_string"
#>
#> $storedFields
#> [1] "location" "name" "uuid"
#> [4] "status" "lsdb" "pubmed_id"
#> [7] "alias_symbol" "ccds_id" "date_approved_reserved"
#> [10] "cosmic" "rna_central_id" "alias_name"
#> [13] "_version_" "date_symbol_changed" "refseq_accession"
#> [16] "locus_type" "bioparadigms_slc" "horde_id"
#> [19] "enzyme_id" "prev_name" "omim_id"
#> [22] "alias_name_string" "gtrnadb" "mgd_id"
#> [25] "homeodb" "symbol" "mane_select"
#> [28] "rgd_id" "entrez_id" "uniprot_ids"
#> [31] "imgt" "hgnc_id" "iuphar"
#> [34] "agr" "gene_group_id" "pseudogene.org"
#> [37] "date_modified" "lncrnadb" "gencc"
#> [40] "locus_group" "orphanet" "mirbase"
#> [43] "location_sortable" "prev_symbol" "curator_notes"
#> [46] "cd" "mamit-trnadb" "ena"
#> [49] "date_name_changed" "ensembl_gene_id" "vega_id"
#> [52] "ucsc_id" "snornabase" "lncipedia"
#> [55] "prev_name_string" "gene_group" "merops"
#>
vgnc_fetch("symbol", "ZNF3")
#> # A tibble: 4 × 19
#> ensembl_gene_id vgnc_id symbol taxonomy_id date_modified locus_group species
#> <chr> <chr> <chr> <int> <chr> <chr> <chr>
#> 1 ENSPTRG000000194… VGNC:1… ZNF3 9598 2016-07-28T0… protein-co… Chimpa…
#> 2 ENSECAG000000246… VGNC:2… ZNF3 9796 2019-01-11T0… protein-co… Horse
#> 3 ENSBTAG000000070… VGNC:3… ZNF3 9913 2019-01-11T0… protein-co… Cattle
#> 4 ENSMMUG000000040… VGNC:8… ZNF3 9544 2019-09-27T0… protein-co… Macaque
#> # ℹ 12 more variables: locus_type <chr>, location <chr>, latin_species <chr>,
#> # ncbi_gene_id <chr>, orthologous_hgnc_id <list>, name <chr>, status <chr>,
#> # date_approved_reserved <chr>, uniprot_id <list>, uuid <chr>,
#> # `_version_` <dbl>, orthologous_gene <list>
vgnc_search(query = "BRAF")
#> vgnc_id symbol taxonomy_id species
#> 1 VGNC:14003 BRAF 9598 Chimpanzee
#> 2 VGNC:15875 BRAF 9796 Horse
#> 3 VGNC:26551 BRAF 9913 Cattle
#> 4 VGNC:38514 BRAF 9615 Dog
#> 5 VGNC:60162 BRAF 9685 Cat
#> 6 VGNC:85866 BRAF 9823 Pig
#> name status score
#> 1 B-Raf proto-oncogene, serine/threonine kinase Approved 177.4734
#> 2 B-Raf proto-oncogene, serine/threonine kinase Approved 177.4734
#> 3 B-Raf proto-oncogene, serine/threonine kinase Approved 177.4734
#> 4 B-Raf proto-oncogene, serine/threonine kinase Approved 177.4734
#> 5 B-Raf proto-oncogene, serine/threonine kinase Approved 177.4734
#> 6 B-Raf proto-oncogene, serine/threonine kinase Approved 177.4734
vgnc_search("symbol", "ZNF*") |>
head()
#> vgnc_id symbol taxonomy_id species name status
#> 1 VGNC:50989 ZNF10 9796 Horse zinc finger protein 10 Approved
#> 2 VGNC:52976 ZNF10 9615 Dog zinc finger protein 10 Approved
#> 3 VGNC:52850 ZNF10 9913 Cattle zinc finger protein 10 Approved
#> 4 VGNC:57802 ZNF10 9598 Chimpanzee zinc finger protein 10 Approved
#> 5 VGNC:111444 ZNF10 9823 Pig zinc finger protein 10 Approved
#> 6 VGNC:11477 ZNF101 9598 Chimpanzee zinc finger protein 101 Approved
#> score
#> 1 1
#> 2 1
#> 3 1
#> 4 1
#> 5 1
#> 6 1
vgnc_search("symbol", c("ZNF*", "AND", "status:Approved")) |>
head()
#> vgnc_id symbol taxonomy_id species name status
#> 1 VGNC:50989 ZNF10 9796 Horse zinc finger protein 10 Approved
#> 2 VGNC:52976 ZNF10 9615 Dog zinc finger protein 10 Approved
#> 3 VGNC:52850 ZNF10 9913 Cattle zinc finger protein 10 Approved
#> 4 VGNC:57802 ZNF10 9598 Chimpanzee zinc finger protein 10 Approved
#> 5 VGNC:111444 ZNF10 9823 Pig zinc finger protein 10 Approved
#> 6 VGNC:11477 ZNF101 9598 Chimpanzee zinc finger protein 101 Approved
#> score
#> 1 1.000014
#> 2 1.000014
#> 3 1.000014
#> 4 1.000014
#> 5 1.000014
#> 6 1.000014