Data Schemas

Details of data frames returned by orphanet-parser. All data is parsed from XML files provided by Orphanet, and column names are preserved (as snake case) to the extent possible. We currently do not sanitize the data, so some inconsistencies present in the Orphanet XML files persist (e.g. yes/no vs y/n for booleans).

For more detailed information on the datasets, see the Orphadata free access product description.

Prevalence

One row represents one prevalence estimate. A disorder may have multiple prevalence estimates.

Column	Description	Values
orphacode	Unique identifier of disorder	int
expert_link	Link to Orphanet page for disase	str
disorder_name	Most generally accepted name of disorder	str
disorder_group	Hierarchical level of the clinical entity.	"Group of disorders" "Disorder" "Subtype of disorder"
prevalence_source	Source of information for prevalence estimate	str
prevalence_type	Type of prevalence estimate	"Point prevalence" "birth prevalence" "lifelong prevalence" "incidence" "cases/families"
prevalence_qualification		"Value and Class" "Only class" "Case" "Family"
prevalence_class	Estimated prevalence	">1 / 1,000" "1-5 / 10,000" "6-9 / 10,000" "1-9 / 100,000" "1-9 / 1,000,000" "<1 /1,000,000" "Not yet documented" "Unknown"
prevalence_geographic	Geographic area of prevalence type	str
prevalence_validation_status	Validation status	"Validated" "Not yet validated"

Natural history

One row represents one disorder, and contains information on the age of onset and type of inheritance.

Column	Description	Values
orphacode	Unique identifier of disorder	int
expert_link	Link to Orphanet page for disase	str
disorder_name	Most generally accepted name of disorder	str
disorder_group	Hierarchical level of the clinical entity	"Group of disorders" "Disorder" "Subtype of disorder"
average_age_of_onset	Groups corresponding to estimated average age of onset. If more than one age of onset is provided, they are alphabetically sorted and semicolon-separated.	"Antenatal" "Neonatal" "Infancy" "Childhood" "Adolescence" "Adult" "Elderly" "All ages" "No data available"
type_of_inheritance	Type of inheritance. If more than one age of onset is provided, they are alphabetically sorted and semicolon-separated.	"Autosomal dominant" "Autosomal recessive" "Multigenic/multifactorial" "Mitochondrial inheritance" "X-linked dominant" "X-linked recessive" "Not applicable" "No data available" "Unknown"

Gene associations

One row represents one association between a gene and disorder.

Column	Description	Values
orphacode	Unique identifier of disorder	int
expert_link	Link to Orphanet page for disase	str
disorder_name	Most generally accepted name of disorder	str
disorder_group	Hierarchical level of the clinical entity	"Group of disorders" "Disorder" "Subtype of disorder"
association_type	Gene-disease relationship	"Biomarker tested in" "Candidate gene tested in" "Disease-causing germline mutation(s) (gain of function) in" "Disease-causing germline mutation(s) (loss of function) in" "Disease-causing germline mutation(s) in" "Disease-causing somatic mutation(s) in" "Major susceptibility factor in" "Modifying germline mutation in" "Part of a fusion gene in" "Role in the phenotype of"
association_status	Gene-disease association status	"Validated" "Not validated"
gene_symbol	HGNC-approved gene symbol	str
gene_name	Full gene name	str
gene_type	Gene type	"gene with protein product" "Non-coding RNA" "Disorder-associated locus"
external_references	List of references in HGNC, OMIM, GenAtlas and UniProtKB, Ensembl, Reactome and IU-PHAR associated with a given gene	str
source_of_validation	Listed reference for a given source associated with a gene	str

Associated phenotypes

One row represents one disorder/phenotype pair. A disorder may have multiple associated phenotypes.

Column	Description	Values
orphacode	Unique identifier of disorder	int
expert_link	Link to Orphanet page for disase	str
disorder_name	Most generally accepted name of disorder	str
disorder_group	Hierarchical level of the clinical entity.	"Group of disorders" "Disorder" "Subtype of disorder"
hpo_id	Unique identifying number assigned by HPO to a given phenotype	str
hpo_term	Preferred name of HPO phenotype	str
hpo_frequency	Estimated frequency of phenotype within disorder	"Obligate (100%)" "Very frequent (99-80%)" "Frequent (79-30%)" "Occasional (29-5%)" "Very rare (<4-1%)" "Excluded (0%)"
diagnostic_criteria	Indicator of phenotype being a pathognomonic sign or a diagnostic criterion in disorder	"Diagnostic criterion" "Pathognomonic sign"
source	Reference	str

Functional consequences

One row represents one disorder/functional consequence pair. A disorder may have multiple functional consequences.

Column	Description	Values
orphacode	Unique identifier of disorder	int
expert_link	Link to Orphanet page for disase	str
disorder_name	Most generally accepted name of disorder	str
disorder_group	Hierarchical level of the clinical entity.	"Group of disorders" "Disorder" "Subtype of disorder"
disability	Name of disability	str
disability_category	Category of disability	“Activity limitation/participation restriction” “No functional disability” “Not applicable”
reason_for_not_applicable	If category is not applicable, the identified reason	“Hypervariable functioning” “Early death-causing disease” “Not applicable for another reason”
frequence_disability	Frequency of the functional consequence in the given population	"very frequent" "frequent" "occasional"
temporality_disability	Temporality of the functional consequence in the given population	“permanent limitation/restriction” “transient limitation/restriction” “delayed acquisition”
severity_disability	Severity of the functional consequence in the given population	“low” “moderate” “severe” “complete” “Unspecified”
loss_of_ability	Defined as a progressive and definitive loss of a skill or ability over the course of the disease	"yes" "no"
type	Disability (functional consequence) or environmental factor	"Disability" "Environmental factor"
defined	Indicator for severity, temporality, and frequency being defined	"y" "n"
source_of_validation	Source of validation of the given clinical entity’s annotation	str
specific_management	If specific management protocol is known for the given disease, this field will indicate “y” for yes and all the annotations will have been conducted considering this specific management protocol.	"y" "n"
annotation_date	Date of annotation	str
status_disability	Status of the validation of the given clinical entity’s annotation	"Validated" "Not validated"