## 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.
[curatedMetagenomicData]: https://www.bioconductor.org/packages/release/data/experiment/html/curatedMetagenomicData.html
[cBioPortalData]: https://www.bioconductor.org/packages/release/bioc/html/cBioPortalData.html
### Installation
```
if (!require("BiocManager"))
install.packages("BiocManager")
BiocManager::install("OmicsMLRepoR")
```
### Harmonized metadata
The harmonized metadata are featured with the following standards:
<img src="https://raw.githubusercontent.com/shbrief/OmicsMLRepoR/master/vignettes/4C_Diagram.png" width="60%" height="60%"/>
### 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.
[OLS]: https://www.ebi.ac.uk/ols4
##### 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"
```
