Annotate Protein Information from Indra

This function standardizes entity identifiers from protein, compound, or gene inputs to a unified namespace using ID conversion from INDRA cogex or Gilda grounding.

Usage

annotateProteinInfoFromIndra(df, proteinIdType)

Arguments

df

output of groupComparison function's comparisonResult table. Must contain a Protein column whose values are interpreted according to proteinIdType. A value may name a protein group – several identifiers for the same quantified analyte joined by ";", e.g. "P13747;P23132" – in which case every member is grounded independently and the results are pooled onto the row.

proteinIdType

A character string specifying the type of analyte identifier in the Protein column. One of "Uniprot", "Uniprot_Mnemonic", "Hgnc_Name", or "Metabolite". The "Metabolite" value treats inputs as metabolite names and grounds them through Gilda, keeping whatever namespace Gilda returns (CHEBI / PUBCHEM / CHEMBL / ...).

Value

A data frame with the following columns:

Protein

Character. The original identifier from the input.

GlobalProtein

Character. The input identifier without the PTM site suffix (typically _<amino acid><site number>, e.g. _S148) stripped from each protein group member, used as the grounding key. NA when the input holds no usable identifier.

UniprotId

Character. The Uniprot ID of the protein, semicolon-joined in the case of multiple proteins, or NA for "Hgnc_Name" and "Metabolite" inputs.

EntityNamespace

Character. The grounding namespace (e.g. "HGNC", "CHEBI"). When a row grounds to multiple candidates – whether from a protein group or from an ambiguous single input – namespaces are semicolon-joined and positionally aligned with EntityId and EntityName.

EntityId

Character. The bare grounding identifier within its namespace (e.g. "1097" for HGNC, "28748" for CHEBI). Semicolon-joined when multi-grounded.

EntityName

Character. The canonical display name from the grounding source. Semicolon-joined when multi-grounded, with "NA" in the positions whose name lookup failed.

IsTranscriptionFactor

Logical. NA for proteinIdType == "Metabolite" and for multi-grounded rows.

IsKinase

Logical. NA for proteinIdType == "Metabolite" and for multi-grounded rows.

IsPhosphatase

Logical. NA for proteinIdType == "Metabolite" and for multi-grounded rows.

Examples

df <- data.frame(Protein = c("CLH1_HUMAN"))
annotated_df <- annotateProteinInfoFromIndra(df, "Uniprot_Mnemonic")
head(annotated_df)
#>      Protein GlobalProtein UniprotId EntityNamespace EntityId EntityName
#> 1 CLH1_HUMAN    CLH1_HUMAN    Q00610            HGNC     2092       CLTC
#>   IsTranscriptionFactor IsKinase IsPhosphatase
#> 1                 FALSE    FALSE         FALSE