ARI Disease Metadata Manager

Public editor: https://aurint.ca/ari-editor/

This repository contains the curated autoimmune disease data, ontology artifacts, and generated reports that support the ARI Disease Metadata Manager v2 shown on the public site.

The editor is the main interface for reviewing and maintaining autoimmune disease metadata. It presents the curated registry as a searchable, editable catalog with disease detail panels and source-linked outputs.

What the editor does

• Search diseases, synonyms, and codes
• Create new disease entries
• Search by symptoms
• Browse diseases alphabetically or by tissue target
• Review disease details in a split-pane layout
• Toggle edit mode for record maintenance
• Adjust settings and theme
• Display supporting panels, graphs, and ontology metadata in the footer

Project scope

This repository supports the curated disease model behind the editor:

• Core disease records with ARI IDs and IRIs
• Synonyms, subtypes, definitions, and evidence metadata
• SNOMED, OMOP, DX code, and DOID mappings
• Proposed diseases and proposed changes
• Supplemental per-disease reports and indexes
• Grounding workflows for local ontology matching

Main directories

Path	Purpose
data/	Master list instructions, report outputs, and supporting source tables
data_model/	Reference spreadsheets and model snapshots
mappings/	ARI equivalency and SSSOM mapping exports
notebook/	Notebook-driven data preparation and grounding scripts
ontologies/	ARI ontology artifacts
sparql/	SPARQL queries and generated term sets

Key outputs

• data/4-reports/1_Core_ARI_Diseases.xlsx
• data/4-reports/2_Proposed_Diseases.xlsx
• data/4-reports/3_Proposed_Changes.xlsx
• data/4-reports/4_Additional_Info_Index.xlsx
• data/4-reports/5_DOID_Mapping.xlsx
• data/4-reports/6_DOID_Matches_All.xlsx
• data/4-reports/7_SNOMED_Matches_All.xlsx

Grounding workflow

The grounding pipeline in notebook/ari-grounding/ builds local DOID and SNOMED matches from repository data only.

Scripts run in this order:

1. parse_doid_local.py
2. ground_doid.py
3. ground_snomed.py
4. make_match_reports.py

Source data

Primary inputs are the master list in data/1-master/ and the supporting files in data/3-meta-database-sources/, ontologies/, mappings/, and sparql/results/.

Mapping validation

.github/scripts/validate_mappings.py checks the two mapping exports against each other and against the ontology. It needs only the standard library:

python .github/scripts/validate_mappings.py

Add --since main to report only the rows a branch changed. Two workflows run it:

Workflow	Trigger	Scope
Validate mappings	pull requests touching mappings/ or ontologies/	rows the branch added or rewrote — fails the check
Audit mappings	Mondays 07:00 UTC, or on demand	every row, so the standing backlog stays visible

What it catches:

• Structural damage — wrong header, wrong column count, stray tabs, mixed line endings, a byte-order mark, a prefix missing from the SSSOM curie_map.
• Identifiers that are not identifiers — mesh:null and other placeholders, doubled prefixes such as MONDO:MONDO:0014523, ids that do not fit their vocabulary's shape, and ICD-9 codes filed under the icd10cm prefix.
• Contradictions — the same pair recorded as both confirmed and flagged wrong, duplicate rows, one disease under two different labels, dates in the future, unattributed edits.
• Drift between ari.sssom.tsv and ari.equivalencies.tsv, which is how spreadsheet round-trips show up: 362.50 losing its trailing zero, 0111157 losing its leading ones.
• Disagreement with the ontology — a disease id or label that does not match, a cross-reference the curators flagged wrong that is still stored and still served, or a confirmed one that was never stored.

Working rules

• Prefer the curated master list as the source of truth.
• Keep changes surgical and focused on one data path at a time.
• Use local ontology and report artifacts rather than online sources when generating matching outputs.
• Do not read .env files unless explicitly authorized.

Related documentation

• Data instructions
• Data overview
• Reports overview