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OmicsMLRepoR

Bioconductor package to access the harmonized metadata through ontology

https://github.com/shbrief/omicsmlrepor

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
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    Committers with academic emails
    2 of 6 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.0%) to scientific vocabulary

Keywords

u24ca289073

Keywords from Contributors

bioconductor-package genomics gene
Last synced: 10 months ago · JSON representation

Repository

Bioconductor package to access the harmonized metadata through ontology

Basic Info
  • Host: GitHub
  • Owner: shbrief
  • Language: R
  • Default Branch: devel
  • Homepage:
  • Size: 16.8 MB
Statistics
  • Stars: 2
  • Watchers: 1
  • Forks: 1
  • Open Issues: 13
  • Releases: 0
Topics
u24ca289073
Created about 3 years ago · Last pushed 12 months ago
Metadata Files
Readme Changelog

README.md

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

B. Harmonized metadata (cmd)

```

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

C. Search descendants of the query in harmonized metadata

```

ontores <- cmd |> treefilter(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"
```

Owner

  • Name: Sehyun Oh
  • Login: shbrief
  • Kind: user
  • Location: New York, NY
  • Company: CUNY-SPH

Molecular Biologist & Bioinformatician

GitHub Events

Total
  • Create event: 12
  • Commit comment event: 1
  • Issues event: 9
  • Watch event: 1
  • Delete event: 15
  • Issue comment event: 6
  • Push event: 30
  • Pull request event: 12
  • Fork event: 1
Last Year
  • Create event: 12
  • Commit comment event: 1
  • Issues event: 9
  • Watch event: 1
  • Delete event: 15
  • Issue comment event: 6
  • Push event: 30
  • Pull request event: 12
  • Fork event: 1

Committers

Last synced: 10 months ago

All Time
  • Total Commits: 194
  • Total Committers: 6
  • Avg Commits per committer: 32.333
  • Development Distribution Score (DDS): 0.273
Past Year
  • Commits: 69
  • Committers: 6
  • Avg Commits per committer: 11.5
  • Development Distribution Score (DDS): 0.188
Top Committers
Name Email Commits
Sehyun Oh s****f@h****m 141
krlong68 k****6@g****m 44
Sehyun Oh s****f@g****m 4
A Wokaty a****y@s****u 2
J Wokaty j****y@s****u 2
Kaelyn Long 9****8@u****m 1
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 2

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 20
  • Total pull requests: 33
  • Average time to close issues: 2 months
  • Average time to close pull requests: 7 days
  • Total issue authors: 2
  • Total pull request authors: 2
  • Average comments per issue: 0.35
  • Average comments per pull request: 0.21
  • Merged pull requests: 29
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 7
  • Pull requests: 12
  • Average time to close issues: 2 months
  • Average time to close pull requests: 14 days
  • Issue authors: 1
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.33
  • Merged pull requests: 10
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • shbrief (19)
  • seandavi (2)
Pull Request Authors
  • krlong68 (24)
  • shbrief (17)
Top Labels
Issue Labels
enhancement (3) help wanted (2) documentation (2) bug (2)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 1,959 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 2
  • Total maintainers: 1
bioconductor.org: OmicsMLRepoR

Search harmonized metadata created under the OmicsMLRepo project

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 1,959 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 31.5%
Average: 42.4%
Downloads: 95.6%
Maintainers (1)
shbrief@gmail.com
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.2.0 depends
  • BiocFileCache * imports
  • DiagrammeR * imports
  • data.tree * imports
  • dplyr * imports
  • jsonlite * imports
  • methods * imports
  • plyr * imports
  • readr * imports
  • rols * imports
  • stats * imports
  • stringr * imports
  • tibble * imports
  • tidyr * imports
  • arrow * suggests
  • testthat >= 3.0.0 suggests