DOI: 10.5281/zenodo.18662231
title: Fabry Disease Case Report Dataset: Structured clinical data from 40 open-access publications

description: Fabry Disease Case Report Dataset

Structured clinical data from open-access case reports, extracted via AI pipeline

Authors



Adrian Michalski (ORCID: 0000-0003-0800-5394)


Abstract

This dataset contains structured clinical phenotype data for 61 patients with Fabry Disease (Anderson-Fabry Disease, OMIM #301500), extracted from 40 open-access case reports indexed in PubMed Central. Data was extracted using the Silene pipeline (Silene Systems), which combines large language model-based information extraction with automated clinical validation and normalization against standard ontologies (HPO, LOINC).

The dataset captures demographics, genetic variants, symptoms, laboratory values, phenotype classifications, and disease staging for each patient. All source publications are open-access and Creative Commons licensed.

Methodology

Data was extracted using a multi-stage AI pipeline (Silene, by Silene Systems):



Search - PubMed Central queried for Fabry Disease case reports using E-utilities API

Screen - AI-based relevance screening to filter case reports with extractable patient-level data

Extract - Structured extraction of patient demographics, genetics, symptoms, and lab values from full-text articles using Claude (Anthropic) with domain-specific prompts

Validate - Automated clinical validation checking internal consistency (e.g., genotype-phenotype concordance, age plausibility, lab value ranges)

Normalize - Symptom names mapped to HPO terms, lab values standardized to canonical names and units, phenotype classification harmonized


Each record includes an extraction_confidence score (model self-assessment) and a data_completeness score (proportion of fields populated).

Data Dictionary

patients.csv / patients.json




Field
Type
Description




case_id
string
Unique patient identifier (format: FAB-NNN)


sex
string
Patient sex: "male" or "female"


age_at_diagnosis
integer
Age in years when Fabry Disease was diagnosed


age_at_symptom_onset
integer
Age in years when first symptoms appeared


genetic_variant
string
GLA gene variant in HGVS coding DNA notation (e.g., c.679C>T)


protein_change
string
Predicted protein change in HGVS notation (e.g., p.R227X)


zygosity
string
Hemizygous (males), heterozygous (females), or homozygous


phenotype
string
Clinical phenotype: "classic", "late-onset", "cardiac", "renal", or "unknown"


disease_stage
string
Disease progression: "early", "moderate", "advanced", or "unknown"


extraction_confidence
float
AI extraction confidence score (0.0-1.0)


data_completeness
float
Proportion of fields successfully extracted (0.0-1.0)


diagnosis_summary
string
Free-text clinical summary of the case




JSON-only nested fields:




Field
Type
Description




symptoms
array
List of symptom objects (see symptoms.csv)


lab_values
array
List of lab value objects (see lab_values.csv)


source
object
Source publication metadata (pmcid, pmid, doi, title, journal, publication_date, license)




symptoms.csv

Long-format table of clinical symptoms per patient.




Field
Type
Description




case_id
string
Patient identifier (FK to patients)


symptom_name
string
Normalized symptom name (mapped to HPO where possible)


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


details
string
Additional clinical details, timing, severity




lab_values.csv

Long-format table of laboratory and clinical measurements.




Field
Type
Description




case_id
string
Patient identifier (FK to patients)


lab_name
string
Normalized lab test name


value
string
Measured value (numeric or descriptive)


unit
string
Unit of measurement


timepoint
string
When the measurement was taken (e.g., "at diagnosis", "6 months post-ERT")


context
string
Additional context (e.g., "reference value < 1.11 ng/mL")




publications.csv

Source publication metadata with enriched identifiers.




Field
Type
Description




pmcid
string
PubMed Central identifier (primary key)


pmid
string
PubMed identifier (enriched via NCBI ID Converter)


doi
string
Digital Object Identifier (enriched via NCBI ID Converter)


title
string
Publication title


journal
string
Journal name


publication_date
string
Publication date (YYYY-MM-DD)


license
string
Creative Commons license type (e.g., CC BY, CC BY-NC)




Dataset Statistics




Metric
Value




Total patients
61


Source publications
40


Male / Female
36 / 22


Mean age at diagnosis
47.6 years


Mean age at symptom onset
31.2 years


Mean extraction confidence
0.90


Mean data completeness
0.61




Field Coverage




Field
Coverage




sex
high


age_at_diagnosis
moderate-high


genetic_variant
moderate-high


protein_change
moderate


phenotype
high (classified for all)


symptoms
high (variable count per patient)


lab_values
moderate (variable count per patient)


age_at_symptom_onset
moderate


zygosity
moderate




Known Limitations



Case report bias - Case reports are published for atypical, severe, or diagnostically challenging presentations. This dataset is not representative of the general Fabry Disease population.

AI extraction errors - Despite validation, AI-extracted data may contain errors. The extraction_confidence score provides a per-record quality indicator but is not a guarantee of accuracy.

Sparse fields - Not all fields are reported in every source publication. data_completeness reflects the proportion of fields populated, but missing data should be treated as unreported, not absent.

Temporal heterogeneity - Source publications span multiple years and reflect different clinical practices, diagnostic criteria, and treatment availability.

Normalization artifacts - Symptom and lab value names have been normalized to canonical forms. Some clinical nuance may be lost in this process; refer to the details and context fields for original descriptions.

Single-gene focus - All patients have Fabry Disease caused by GLA gene variants. The dataset structure could support other lysosomal storage disorders but currently only contains Fabry Disease data.


License

The structured data in this dataset is released under CC BY 4.0 (Creative Commons Attribution 4.0 International).

All source publications are open-access and published under Creative Commons licenses (CC BY, CC BY-NC, CC BY-NC-ND, CC BY-NC-SA). The extracted factual data (clinical observations, measurements, genetic variants) is not subject to copyright per the fact/expression dichotomy. The structured compilation is an original work licensed CC BY 4.0.

Suggested Citation



Michalski, A. (2026). Fabry Disease Case Report Dataset: Structured clinical data from 40 open-access publications. Zenodo. https://doi.org/10.5281/zenodo.18662232


Extraction Pipeline

This dataset was generated using Silene Systems (https://github.com/amichalski/silene-case-study), an AI-powered pipeline for extracting structured clinical data from medical case reports.

File Manifest




File
Format
Description




patients.json
JSON
Full dataset with nested symptoms, lab values, and source metadata


patients.csv
CSV
Flat patient demographics and genetics table


symptoms.csv
CSV
Long-format symptom presence/absence per patient


lab_values.csv
CSV
Long-format laboratory measurements per patient


publications.csv
CSV
Source publication metadata with enriched identifiers


README.md
Markdown
This data descriptor




Contact

For questions about this dataset, please contact the author via ORCID.