metadata-harmonization-starter

Name: metadata-harmonization-starter
Author: ma-compbio-lab

36stars5forks

How to install metadata-harmonization-starter?

ma-compbio-lab/skillfoundry/metadata-harmonization-starter

$npx -y skills add ma-compbio-lab/SkillFoundry --skill metadata-harmonization-starter

Installs into the current project.

Summary

Use this skill to harmonize small metadata tables with inconsistent column names and categorical labels into one canonical TSV plus a compact JSON summary.

Files · 1

View on GitHub

SKILL.md

1	# Metadata Harmonization Starter
2
3	Use this skill to harmonize small metadata tables with inconsistent column names and categorical labels into one canonical TSV plus a compact JSON summary.
4
5	## What This Skill Does
6
7	- reads one or more tabular metadata files
8	- applies a JSON mapping from source columns to canonical fields
9	- normalizes selected categorical values such as `sex` and `condition`
10	- writes a harmonized TSV and a machine-readable summary
11
12	## When To Use It
13
14	- when you need a starter for `metadata-harmonization`
15	- when multiple small test fixtures use different metadata headers
16	- when you want deterministic harmonized outputs before validation or format conversion
17
18	## Run
19
20	```bash
21	python3 skills/data-acquisition-and-dataset-handling/metadata-harmonization-starter/scripts/run_metadata_harmonization.py \
22	--input skills/data-acquisition-and-dataset-handling/metadata-harmonization-starter/examples/cohort_a.tsv \
23	--input skills/data-acquisition-and-dataset-handling/metadata-harmonization-starter/examples/cohort_b.tsv \
24	--mapping skills/data-acquisition-and-dataset-handling/metadata-harmonization-starter/examples/column_mapping.json \
25	--out-tsv scratch/metadata-harmonization/harmonized_metadata.tsv \
26	--summary-out scratch/metadata-harmonization/harmonized_metadata_summary.json
27	```
28
29	## Notes
30
31	- The starter keeps the mapping external so the same script can be reused for other tiny fixtures.
32	- Canonical rows are sorted by `sample_id` to keep committed outputs deterministic.

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metadata-harmonization-starter

36stars5forks

View on GitHub

How to install metadata-harmonization-starter?

ma-compbio-lab/skillfoundry/metadata-harmonization-starter

$npx -y skills add ma-compbio-lab/SkillFoundry --skill metadata-harmonization-starter

Installs into the current project.

Summary

Use this skill to harmonize small metadata tables with inconsistent column names and categorical labels into one canonical TSV plus a compact JSON summary.

Files · 1

View on GitHub

SKILL.md

1	# Metadata Harmonization Starter
2
3	Use this skill to harmonize small metadata tables with inconsistent column names and categorical labels into one canonical TSV plus a compact JSON summary.
4
5	## What This Skill Does
6
7	- reads one or more tabular metadata files
8	- applies a JSON mapping from source columns to canonical fields
9	- normalizes selected categorical values such as `sex` and `condition`
10	- writes a harmonized TSV and a machine-readable summary
11
12	## When To Use It
13
14	- when you need a starter for `metadata-harmonization`
15	- when multiple small test fixtures use different metadata headers
16	- when you want deterministic harmonized outputs before validation or format conversion
17
18	## Run
19
20	```bash
21	python3 skills/data-acquisition-and-dataset-handling/metadata-harmonization-starter/scripts/run_metadata_harmonization.py \
22	--input skills/data-acquisition-and-dataset-handling/metadata-harmonization-starter/examples/cohort_a.tsv \
23	--input skills/data-acquisition-and-dataset-handling/metadata-harmonization-starter/examples/cohort_b.tsv \
24	--mapping skills/data-acquisition-and-dataset-handling/metadata-harmonization-starter/examples/column_mapping.json \
25	--out-tsv scratch/metadata-harmonization/harmonized_metadata.tsv \
26	--summary-out scratch/metadata-harmonization/harmonized_metadata_summary.json
27	```
28
29	## Notes
30
31	- The starter keeps the mapping external so the same script can be reused for other tiny fixtures.
32	- Canonical rows are sorted by `sample_id` to keep committed outputs deterministic.

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6 picks

Type