Mic Nutrient Creation

Check if it already exists:

ls kb/nutrients/**/*.yaml

Step 2: Mark as In Progress

Update CURATION-PROGRESS.md to mark the nutrient as in progress:

1. Find the nutrient's line in the file
2. Change [ ] to [~] to indicate work has started
3. Optionally add a note about what's being worked on

Example: Change this line:

- [ ] Folate (`kb/nutrients/vitamins/folate.yaml`)

To:

- [~] Folate (`kb/nutrients/vitamins/folate.yaml`) - in progress

This helps track curation status and prevents duplicate work.

Step 3: Fetch MIC Page Content

Download the MIC page using the just fetch-mic-page command:

# Format: just fetch-mic-page {category}/{nutrient}
just fetch-mic-page vitamins/biotin
just fetch-mic-page minerals/calcium
just fetch-mic-page dietary-factors/lipoic-acid

This downloads the HTML to cache/mic-pages/{nutrient}.html.

Verify the download:

ls -la cache/mic-pages/biotin.html

Step 4: Extract Reference Mapping

IMPORTANT: Before adding evidence, extract the MIC reference number → PMID mapping:

# Get TSV mapping of ref# to PMID
just extract-refs cache/mic-pages/biotin.html

This outputs a TSV with columns: source, reference_number, pubmed_id, citation

Example output:

source          reference_number  pubmed_id       citation
biotin.html     1                               Zempleni J, Wijeratne SSK...
biotin.html     2                 PMID:10357733  Mock DM. Biotin...
biotin.html     3                 PMID:15992684  Zempleni J, Hassan YI...

Key points:

• Empty pubmed_id = book chapter or non-PMID source (use mic_references only)
• Has pubmed_id = can fetch abstract and add PMID evidence
• The reference_number corresponds to mic_references values in the YAML

Save the mapping for reference during curation:

just extract-refs cache/mic-pages/biotin.html > cache/refs/biotin-refs.tsv

Step 5: Create Initial YAML File

Create kb/nutrients/{category}/{nutrient}.yaml with the basic structure: