DOI: 10.5281/zenodo.18799012
title: Fabry Disease: AI-Extracted Clinical Dataset from Published Case Reports

description: General Information



Title: Fabry Disease: AI-Extracted Clinical Dataset from Published Case Reports

Version: 1.0.0

Date of export: 2026-02-27

Created by: Silene Systems (AI-powered clinical data extraction pipeline)

Disease: Fabry Disease (OMIM #301500)

Gene: GLA (Xq22.1)

Inheritance: X-linked


Description

This dataset contains structured clinical data for 154 patients with Fabry disease, automatically extracted from 93 peer-reviewed case reports and case series indexed in PubMed Central. Data was extracted using a multi-agent AI pipeline with automated validation, clinical plausibility checks, and human review.

Each patient record includes demographics, genetic variants, clinical symptoms with temporal information, laboratory values, and links to source publications. Symptoms are provided in two formats: original AI-extracted terms and HPO (Human Phenotype Ontology)-normalized mappings with confidence scores.

The dataset is intended for rare disease research, phenotype-genotype correlation studies, natural history analysis, and machine learning applications in clinical genetics.

Dataset Summary




Metric
Value




Patients
154


Publications
93


Symptom observations (original)
2,039


Symptom observations (HPO-normalized)
2,017


Unique symptom names
803


Lab value measurements
1,264


Patients with genetic variant
103


Unique genetic variants
60




Demographics




 
Count




Male
73


Female
73


Unknown sex
8




 




Age metric
Available
Min
Max
Median




Age at symptom onset
54
0
74
36


Age at diagnosis
124
4
75
48




Phenotype Distribution




Phenotype
Count




Classic
66


Later-onset
67


Asymptomatic carrier
1




File Descriptions

patients.csv (154 rows)

One row per patient. Contains demographics, genetics, and clinical summary.




Column
Type
Description




case_id
string
Unique patient identifier (e.g., FAB-001)


sex
string
Patient sex (male/female)


age_at_symptom_onset
numeric
Age in years at first symptom onset


age_at_diagnosis
numeric
Age in years at Fabry disease diagnosis


diagnostic_delay_years
numeric
Difference between diagnosis and onset age


genetic_variant
string
GLA gene variant in HGVS notation (e.g., c.644A>G)


protein_change
string
Protein-level change (e.g., p.Asn215Ser)


zygosity
string
Hemizygous, heterozygous, or homozygous


phenotype
string
Clinical phenotype: classic, later-onset, or asymptomatic carrier


disease_stage
string
Disease stage if reported


diagnosis_summary
string
AI-generated clinical summary


extraction_confidence
numeric
AI extraction confidence score (0-1)


data_completeness
numeric
Proportion of fields populated (0-1)


publication_pmcid
string
PubMed Central ID of source publication




symptoms.csv (2,039 rows)

One row per symptom observation, sourced from the original AI extraction. Preserves the exact clinical terminology used in source publications.




Column
Type
Description




case_id
string
Patient identifier


symptom_name
string
Original symptom name as extracted from the publication


present
boolean
Whether the symptom is present (True) or explicitly absent (False)


details
string
Additional clinical details or context


timepoint_raw
string
Raw temporal reference from the publication


timepoint_category
string
Normalized category: onset, diagnosis, follow_up, etc.


age_at_event
numeric
Patient age at the time of this observation


offset_months
numeric
Months relative to a reference event




symptoms_hpo.csv (2,017 rows)

One row per symptom mapped to the Human Phenotype Ontology (HPO). Enables standardized phenotype analysis and cross-dataset comparisons. HPO mappings have been validated and corrected using LLM-based quality review.




Column
Type
Description




case_id
string
Patient identifier


original_name
string
Original symptom name from the publication


canonical_name
string
HPO-normalized term name


hpo_id
string
HPO identifier (e.g., HP:0001639)


present
boolean
Whether the symptom is present (True) or absent (False)


details
string
Additional clinical details


timepoint
string
Temporal reference


context
string
Clinical context


confidence
numeric
Mapping confidence score (0-1)




lab_values.csv (1,264 rows)

One row per laboratory measurement or diagnostic test result.




Column
Type
Description




case_id
string
Patient identifier


lab_name
string
Name of the laboratory test or biomarker


value
string
Measured value (numeric or descriptive)


unit
string
Unit of measurement


context
string
Clinical context (e.g., baseline, post-treatment)


timepoint_raw
string
Raw temporal reference


timepoint_category
string
Normalized temporal category


age_at_event
numeric
Patient age at measurement


offset_months
numeric
Months relative to a reference event




publications.csv (93 rows; 95 with header)

One row per source publication.




Column
Type
Description




pmcid
string
PubMed Central ID


pmid
string
PubMed ID


doi
string
Digital Object Identifier


title
string
Publication title


authors
string
Author list (semicolon-separated)


journal
string
Journal name


publication_date
date
Publication date (YYYY-MM-DD)


license
string
Publication license




dataset_summary.json

Machine-readable summary with aggregate statistics including patient counts, demographic distributions, genetic variant counts, and phenotype breakdown.

Methodology

Data Extraction Pipeline



Publication Discovery — Automated PubMed search for Fabry disease case reports (publications from 2015 onwards)

Relevance Screening — AI-based abstract screening to filter relevant case reports

Case Extraction — Structured patient data extraction from full-text articles using Claude Opus 4.6 (Claude, Anthropic)

Clinical Validation — Automated checks for temporal logic, lab value plausibility, and genetic consistency against disease-specific profiles

HPO Normalization — Mapping of extracted symptom terms to Human Phenotype Ontology, with LLM-based validation and correction of mappings

Timepoint Normalization — Structuring of free-text temporal references into standardized categories with chronological ordering


Quality Assurance



Extraction confidence and data completeness scores per patient

Automated clinical plausibility validation

HPO mapping quality validated by LLM review

Negated findings (symptoms explicitly absent) are captured with present=False

Manual audit of random samples against source publications confirmed >90% symptom completeness and near-complete laboratory value extraction


Limitations



Data quality depends on the detail and clarity of source publications

Some clinical findings may be missed if not explicitly stated in the text

HPO mappings for ~246 symptoms lack HPO IDs (canonical name provided but ID not in reference ontology)

Temporal information is not always available or precisely reported in source publications

Dataset is limited to publications indexed in PubMed Central with available full text


License

The structured data in this dataset is derived from published scientific literature. Individual source publications retain their original licenses (see publications.csv). This compiled dataset is made available under CC BY 4.0.