Introduction

Databases use identifiers to point to records. One of the goals of BridgeDb is is to map identifier for a record from one database to the identifier of a matching record in another database. This is explained in the Tutorial vigenette.

However, within one databases, linking from one identifier to another can also be useful. Many databases have older and newer identifiers, where the newer identfier replaces the older identifier. For example, HGNC replaces symbols to make naming more consistent or to solve ambiguity.

The recent sec2pri and BridgeDb Tiwid projects track outdated identifiers. These projects define secondary identifiers as identifiers that should not be used anymore. Some of them have been replaced by new identifiers, called primary identifiers.

This vignette explains how to use sec2pri BridgeDb identifier mapping files to detect secondary identifiers, and, where possible, suggest the replacing primary identifier.

The Bioconductor BridgeDbR package page describes how to install the package. After installation, the library can be loaded with the following command:

install.packages("BiocManager")
BiocManager::install("BridgeDbR")
install.packages(pkgs=c("rJava", "curl"))

library(curl)
library(rJava)
library(BridgeDbR)

*Note: if you have trouble with rJava (required package), please read the general information or follow the instructions here for Ubuntu.

Downloading sec2pri databases

The first thing to do is download a BridgeDb identifier mapping database. This database is a .bridge file just as those from the BridgeDb website. The difference is that these sec2pri databases focus on primary and secondary identifiers of a single data source.

Here we will use ChEBI (Hastings et al. 2016) as an example. These files can be downloaded as artifacts produced during one of the GitHub Actions in the mapping_preprocessing repository, specifically, here.

Click the most recently run Check and test ChEBI updates run, and notice the artifacts:

Click the chebi_procesed artifact and save this locally as a chebi_processed.zip file. Unzip the file to get the ChEBI_secID2priID.bridge file in the current working directory.

Loading the sec2pri database

This downloaded file is then loaded with (see also the Tutorial vignette):

sec2pri = BridgeDbR::loadDatabase("ChEBI_secID2priID.bridge")

Analyzing ChEBI identifiers

Let’s say we have the ChEBI identifier CHEBI:1234 in our dataset and we want to know if this is a primary or a secondary identifier. We can check with the sec2pri databases which other identifiers it is mapped to:

BridgeDbR::map(sec2pri, source="Ce", identifier="CHEBI:1234")

The output looks like this:

  source identifier target     mapping isPrimary
1     Ce CHEBI:1234     Ce  CHEBI:1234         F
2     Ce CHEBI:1234     Ce CHEBI:19730         F
3     Ce CHEBI:1234     Ce CHEBI:28423         T

Two first two columns are your input identifier, and column three and four are mapped identifiers. The fifth column indicates if the column is primary (T) or secondary (F). We see here that CHEBI:1234 is a secondary identifier.

We also see that there is a matching primary identifier, CHEBI:28243.

We can extract the primary identifier with regular R code, e.g. like:

mappedIDs = BridgeDbR::map(sec2pri, source="Ce", identifier="CHEBI:1234")
mappedIDs[intersect(which(mappedIDs[,"target"] == "Ce"),which(mappedIDs[,"isPrimary"] == "T")),]

Conclusion

With the appropriate sec2pri you can use this approach to identify secondary identifiers, and where possible, replace them with the matching primary identifier.

Please keep in mind, most databases have their own reasons for when to replace an identifier, and rules how to do that. Some databases do not, however, have 1-to-1 relationships, and manual inspection is recommended.

References

Session info

Here is the output of sessionInfo() on the system on which this document was compiled running pandoc 3.6.3:

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Hastings, Janna, Gareth Owen, Adriano Dekker, Marcus Ennis, Namrata Kale, Venkatesh Muthukrishnan, Steve Turner, Neil Swainston, Pedro Mendes, and Christoph Steinbeck. 2016. “ChEBI in 2016: Improved Services and an Expanding Collection of Metabolites.” Nucleic Acids Research 44 (D1): D1214–9. https://doi.org/10.1093/NAR/GKV1031.