ICAM Library Metadata

Overview

This vignette describes the metadata fields provided with the ICAM PhIP-seq peptide library. The metadata combine peptide-level information, source-protein sequences, taxonomic annotations, library-construction labels, and information about fused protein fragments. The library can be retrieved via phiperio’s get_peptide_library():

library(phiperio)
library(phiper)
library(dplyr)

peplib <- get_peptide_library("icam") %>%
  collect()
#> [17:15:58] INFO  Retrieving peptide metadata into DuckDB cache
#>                  -> get_peptide_library(library = icam, force_refresh = FALSE)
#> [17:15:58] INFO  Opened DuckDB connection
#>                    - cache dir:
#>                      /home/runner/.cache/R/phiperio/peptide_meta/phip_cache.duckdb
#>                    - tables: peptide_meta_icam
#> [17:15:58] INFO  Starting download
#>                    - dest:
#>                      /home/runner/.cache/R/phiperio/peptide_meta/icam_library_01.10.26.rds
#> [17:15:59] OK    Download succeeded (method = <getOption()>)
#> [17:15:59] OK    Checksum verified (SHA-256 match)
#> [17:16:04] OK    Download complete and loaded into R
#> [17:16:08] INFO  Importing sanitized metadata into DuckDB cache...
#> [17:16:11] OK    peptide_meta_icam table created in DuckDB cache
#> [17:16:11] OK    Retrieving peptide metadata into DuckDB cache - done
#>                  -> elapsed: 13.038s

All columns beginning with is_ are binary dummy variables: 1 indicates that the corresponding annotation applies to the peptide/protein, 0 indicates that it does not.

General library information

The following columns describe peptide-level and source-protein information.

Column	Description
peptide_id	Unique peptide identifier in the ICAM library. Final IDs use the format icam_<number>.
aa_seq	Amino-acid sequence of the encoded peptide/oligo.
pos	0-based start position of the selected peptide mapping within the full original source-protein sequence. When multiple valid mappings existed, the first retained position is used in the final table.
len_seq	Length, in amino acids, of the full original source-protein sequence.
full_aa_seq	Full amino-acid sequence of the original source protein. Not included in the library served by phiperio because of large file size.
Description	Protein annotation/description associated with the peptide, derived from the original PGAP annotation within each proteome downloaded from GenBank or RefSeq. This corresponds to the protein description previously stored as Fullname.

Taxonomic information

Taxonomic lineage fields were harmonized using NCBI taxonomy where possible. The normalized species field and the original species_exact field are intentionally retained separately.

Column	Description
tax_id	NCBI Taxonomy identifier assigned during taxonomic harmonization, when available.
domain	Highest-level taxonomic assignment used in the metadata, e.g. Bacteria, Archaea, Eukaryota, or Viruses.
kingdom	Taxonomic kingdom, when available in the NCBI lineage.
phylum	Taxonomic phylum.
class	Taxonomic class.
order	Taxonomic order.
family	Taxonomic family.
genus	Taxonomic genus.
species	Taxonomic species.
species_exact	Original organism name retained from the source annotation (the strain name found in the GenBank file of the downloaded strain). This may preserve strain, subspecies, isolate, or historical naming information not present in the normalized species field.

Library annotation flags

The following fields derive from annotation labels carried through the ICAM library-construction workflow. They can be used to filter peptides by control set, disease-associated mimotope set, protein function, predicted function, localization, or curated library component.

Column	Description
is_Controls_Agilent	Peptides belonging to the Agilent control set.
is_Controls_Israeli_Common_epitopes	Peptides belonging to the Israeli common-epitope control set (epitopes found at 5-95% prevalence in an Israeli cohort).
is_Controls_Random	Random control peptides.
is_EBV_variants	Epstein-Barr virus (EBV) variant peptides.
is_MS_mimotope	Peptides annotated as multiple sclerosis (MS) mimotopes.
is_RA_mimotope	Peptides annotated as rheumatoid arthritis (RA) mimotopes.
is_SARS_CoV_variants	SARS-CoV variant peptides.
is_SLE_mimotope	Peptides annotated as systemic lupus erythematosus (SLE) mimotopes.
is_SSc_mimotope_100	Peptides in the systemic sclerosis (SSc) mimotope set labelled 100.
is_SSc_mimotope_90	Peptides in the systemic sclerosis (SSc) mimotope set labelled 90.
is_adhesin	Peptides derived from proteins identified as adhesins.
is_aeromonas_aerolysin	Peptides belonging to the Aeromonas aerolysin annotation set.
is_agilent_flagellins	Peptides belonging to the Agilent flagellin annotation set.
is_antibiotic_resistance	Proteins predicted as antibiotic-resistance related using DIAMOND against the curated CARD database.
is_axSpA_mimotope	Peptides annotated as axial spondyloarthritis (axSpA) mimotopes.
is_crc_proteins	Proteins included in the colorectal cancer (CRC)-associated protein set used during library construction.
is_flagellin	Proteins identified as flagellins within the initial PGAP annotations.
is_fusobacterium_orthologues	Peptides/proteins belonging to the Fusobacterium subspecies orthologue set.
is_immunogenic_proteins	Proteins included in the immunogenic-protein annotation set.
is_invasion_proteins	Proteins annotated as invasion-related proteins.
is_ley_flagellins	Peptides belonging to the Ley flagellin annotation set.
is_membrane	Proteins annotated as membrane-associated.
is_predicted_antibiotic_resistance	Proteins computationally predicted to be antibiotic-resistance related.
is_predicted_flagellin	Proteins predicted as flagellins using DIAMOND against a bacterial flagella database downloaded from UniProt.
is_predicted_toxin	Proteins computationally predicted to be toxins.
is_secreted	Proteins annotated or predicted as secreted.
is_ureases	Proteins belonging to the urease annotation set.

Fused-protein information

Some ICAM library entries were constructed by joining multiple protein fragments with a linker. The following field preserves the original location of each component fragment.

Column	Description
origin_fused_chunks	For peptides derived from fused library proteins, the source chunk origins as a list of (original_protein_id, start_position) tuples. Start positions are 0-based coordinates in the full original protein. The field may contain two, three, or more tuples depending on the number of fragments used in the fusion. For non-fused proteins it is not applicable and may be empty/NA.

Credits

This documentation of the ICAM library metadata fields was written by Gabriel Innocenti.