Improved findability and AI/ML-readiness of non-omics metadata

The OmicsMLRepo project aims to harmonize and standardize clinical metadata from public Omics data resources. Currently, curatedMetagenomicData and the part of cBioPortalData's metadata are processed under this project.

Installation

if (!require("BiocManager"))
    install.packages("BiocManager")

BiocManager::install("OmicsMLRepoR")

Harmonized metadata

The harmonized metadata are featured with the following standards:

Rubust data searching

OmicsMLRepoR is the R package to facilitate the easy access and search of the harmonized metadata produced under the OmicsMLRepo project. Thanks to the ontology, metadata searching in OmicsMLRepoR is much more robust - your query automatically includes OLS-defined synonyms (Example B) and all the descendants (Example C) from the ontology tree.

A. Before harmonization (original metadata, sampleMetadata)

> library(curatedMetagenomicData)
> nrow(sampleMetadata |> filter(study_condition == "CRC"))
[1] 701
> nrow(sampleMetadata |> filter(disease == "CRC"))
[1] 625
> nrow(sampleMetadata |> filter(study_condition == "crc"))
[1] 0
> nrow(sampleMetadata |> filter(study_condition == "Colorectal Carcinoma"))
[1] 0
> nrow(sampleMetadata |> filter(study_condition == "Colorectal Cancer"))
[1] 0
> nrow(sampleMetadata |> filter(study_condition == "Intestinal Disorder"))
[1] 0

B. Harmonized metadata (cmd)

> library(OmicsMLRepoR)
> cmd <- getMetadata("cMD")
> nrow(cmd |> tree_filter(disease, "CRC"))
[1] 701
> nrow(cmd |> tree_filter(disease, "crc")) # not case-sensitive
[1] 701
> nrow(cmd |> tree_filter(disease, "Colorectal Carcinoma")) # synonym
[1] 701
> nrow(cmd |> tree_filter(disease, "Colorectal Cancer")) # synonym
[1] 701

C. Search descendants of the query in harmonized metadata

> onto_res <- cmd |> tree_filter(disease, "Intestinal Disorder")
> unique(onto_res$disease)
 [1] "Crohn Disease;Schizophrenia"                                                           
 [2] "Colorectal Carcinoma;Hepatic Steatosis;Hypertension;Carcinoma"                         
 [3] "Colorectal Carcinoma;Carcinoma"                                                        
 [4] "Colorectal Carcinoma;Type 2 Diabetes Mellitus;Hepatic Steatosis;Hypertension;Carcinoma"
 [5] "Colorectal Carcinoma;Hypertension;Carcinoma"                                           
 [6] "Colorectal Carcinoma;Hepatic Steatosis;Carcinoma"                                      
 [7] "Colorectal Carcinoma;Type 2 Diabetes Mellitus;Hypertension;Carcinoma"                  
 [8] "Colorectal Carcinoma;Adenocarcinoma"                                                   
 [9] "Inflammatory Bowel Disease;Crohn Disease"                                              
[10] "Inflammatory Bowel Disease;Ulcerative Colitis"                                         
[11] "Colorectal Carcinoma"                                                                  
[12] "Cytomegaloviral Infection;Celiac Disease;Gestational Diabetes"                         
[13] "Type 1 Diabetes Mellitus;Celiac Disease;Irritable Bowel Syndrome"                      
[14] "Inflammatory Bowel Disease"                                                            
[15] "Inflammatory Bowel Disease;Fecal Microbiota Transplantation"                           
[16] "Melanoma;Colitis"                                                                      
[17] "Inflammatory Bowel Disease;Anorectal Fistula;Crohn Disease"                            
[18] "Colorectal Carcinoma;Hypercholesterolemia;Adenocarcinoma"                              
[19] "Colorectal Carcinoma;Hypertension;Adenocarcinoma"                                      
[20] "Colorectal Carcinoma;Hypercholesterolemia;Hypertension;Adenocarcinoma"                 
[21] "Colorectal Carcinoma;Metastatic Malignant Neoplasm;Adenocarcinoma"                     
[22] "Inflammatory Bowel Disease;Colitis"                                                    
[23] "Colorectal Carcinoma;Type 2 Diabetes Mellitus;Carcinoma"                               
[24] "Adenoma;Small Intestinal Adenoma"                                                      
[25] "Adenoma;Colorectal Adenoma"