Convert Identifiers in Biological Databases

Identifiers in biological databases connect different levels of metadata, phenotype data or genotype data. This tool is designed to easily convert identifiers within or between different biological databases (Wang, Shixiang, et al. (2021) ).

IDConverter

The goal of IDConverter is to convert identifiers between biological databases. Currently, I mainly use it for promoting cancer study.

Installation

Install the latest version of IDConverter in GitHub with:

remotes::install_github("WangLabCSU/IDConverter")

Or Gitee (better in China, but updates may lag behind):

remotes::install_git("https://gitee.com/ShixiangWang/IDConverter")

Available features

ID conversions:

• convert_custom() - Convert custom database identifiers.
• convert_icgc() - Convert ICGC identifiers.
• convert_pcawg() - Convert PCAWG identifiers.
• convert_tcga() - Convert TCGA identifiers.
• convert_hm_genes() - Convert human/mouse/worm gene IDs between Ensembl and Hugo Symbol system.
• convert_hm_orthologs() - Convert gene IDs between human and mouse via Ensembl orthology (e.g., TP53 ↔ Trp53).

Annotation tables:

• ls_annotables() - List available annotation tables from annotables.
• load_data() - Download and load annotation data from Zenodo (fixed version) or from local cache.
• build_annotables() - Build up-to-date gene annotation tables directly from Ensembl BioMart (supports 11 organisms, requires biomaRt).
• resolve_gene_aliases() - Resolve outdated/alternative gene symbols (aliases) to official symbols via Ensembl synonym data.

Utilities:

• pair_gdc_samples() - Pair tumor-normal samples from GDC manifest files.
• parse_gdc_file_uuid() - Parse Metadata from GDC Portal File UUID.
• filter_tcga_barcodes() - Filter TCGA Replicate Sample Barcodes.

Examples

library(IDConverter)

To follow the CRAN policy, I have to set tempdir() as default data path, however, I recommend you set the data path to a specified path with options(IDConverter.datapath).

e.g.,

options(IDConverter.datapath = system.file("extdata", package = "IDConverter"))

TCGA

x <- convert_tcga("TCGA-02-0001-10")
x
#> [1] "TCGA-02-0001"

PCAWG

x <- convert_pcawg("SP1677")
x
#> [1] "DO804"

ICGC

x <- convert_icgc("SP29019")
x
#> [1] "DO13695"

Genes

convert_hm_genes(c("TP53", "KRAS", "EGFR", "MYC"), type = "symbol")
#> Downloading https://zenodo.org/records/10360995/files/human_hg38_gene_info.rds to /private/var/folders/1w/371ktd8j0fv8mp_dsgtvssnw0000gn/T/RtmpMMmC4n/temp_libpath4f1e764f17f3/IDConverter/extdata/human_hg38_gene_info.rds
#> [1] "ENSG00000141510" "ENSG00000133703" "ENSG00000146648" "ENSG00000136997"

# Or use data from annotables
ls_annotables()
#> Downloading https://zenodo.org/records/10360995/files/ensembl_version.rda to /private/var/folders/1w/371ktd8j0fv8mp_dsgtvssnw0000gn/T/RtmpMMmC4n/temp_libpath4f1e764f17f3/IDConverter/extdata/ensembl_version.rda
#> Version: Ensembl Genes 105
#>  [1] "bdgp6"            "bdgp6_tx2gene"    "galgal5"          "galgal5_tx2gene" 
#>  [5] "grch37"           "grch37_tx2gene"   "grch38"           "grch38_tx2gene"  
#>  [9] "grcm38"           "grcm38_tx2gene"   "mmul801"          "mmul801_tx2gene" 
#> [13] "rnor6"            "rnor6_tx2gene"    "wbcel235"         "wbcel235_tx2gene"
grch37 = load_data("grch37")
#> Downloading https://zenodo.org/records/10360995/files/grch37.rda to /private/var/folders/1w/371ktd8j0fv8mp_dsgtvssnw0000gn/T/RtmpMMmC4n/temp_libpath4f1e764f17f3/IDConverter/extdata/grch37.rda
head(grch37)
#> # A tibble: 6 × 9
#>   ensgene         entrez symbol   chr    start    end strand biotype description
#>   <chr>            <int> <chr>    <chr>  <int>  <int>  <int> <chr>   <chr>      
#> 1 ENSG00000000003   7105 TSPAN6   X     1.01e8 1.01e8     -1 protei… tetraspani…
#> 2 ENSG00000000005  64102 TNMD     X     1.01e8 1.01e8      1 protei… tenomodulin
#> 3 ENSG00000000419   8813 DPM1     20    5.09e7 5.10e7     -1 protei… dolichyl-p…
#> 4 ENSG00000000457  57147 SCYL3    1     1.70e8 1.70e8     -1 protei… SCY1 like …
#> 5 ENSG00000000460  55732 C1orf112 1     1.70e8 1.70e8      1 protei… chromosome…
#> 6 ENSG00000000938   2268 FGR      1     2.76e7 2.76e7     -1 protei… FGR proto-…
convert_custom(c("TP53", "KRAS", "EGFR", "MYC"),
               from = "symbol", to = "entrez", dt = grch37)
#> [1] "7157" "3845" "1956" "4609"

Human-Mouse Orthologs

# Human → Mouse
convert_hm_orthologs(c("TP53", "KRAS", "EGFR", "MYC"))
# => Trp53, Kras, Egfr, Myc

# Mouse → Human
convert_hm_orthologs(c("Trp53", "Kras"), from_species = "mouse", to_species = "human")
# => TP53, KRAS

# Ensembl ID mapping
convert_hm_orthologs("ENSG00000141510", from_type = "ensembl", to_type = "ensembl")
# => ENSMUSG00000059552

Gene Symbol Aliases

# Build annotation table with synonym support
ann <- build_annotables("grch38", include_synonyms = TRUE, tx2gene = FALSE)

# Resolve aliases (e.g., old names → official symbols)
resolve_gene_aliases(c("TP53", "T245", "MLL"), ann[[1]])
# T245 → TSPAN6, MLL → KMT2A (if in synonym data)

GDC Manifest Pairing

# Pair tumor-normal samples from a GDC manifest file
info <- pair_gdc_samples("gdc_manifest.txt")
head(info)

Citation

Wang S, Li H, Song M, Tao Z, Wu T, He Z, et al. (2021) Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes. PLoS Genet 17(5): e1009557. https://doi.org/10.1371/journal.pgen.1009557

Similar package

• AnnoProbe (Gitee mirror) is an R package for transforming Chips probes to different Gene IDs.

LICENSE

MIT@2020, Shixiang Wang