Tutorials
The OrphanetData class provides access to all the individual data frames. By default, the latest version is used, currently "2024-07".
The following sections walk through examples of analyses one might want to do with the orphanet-parser package.
Finding disorders associated with a gene
Imagine we are interested in finding information about disorders associated with a particular disease. We can query the gene associations data by gene symbol.
gene_df = orphanet.gene_associations()
smn1_disorders = gene_df[ gene_df['gene_symbol'] == 'SMN1' ].copy()
In the case of SMN1, there are four associated disorders: Proximal spinal muscular atrophy type 1-4. These are all classified as subtypes of a disorder, and are caused by germline mutations in the SMN1 gene.
| orphacode | expert_link | disorder_name | disorder_type | disorder_group | association_type | association_status | gene_symbol | gene_name | gene_type | external_references | source_of_validation |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 83330 | http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=83330 | Proximal spinal muscular atrophy type 1 | Clinical subtype | Subtype of disorder | Disease-causing germline mutation(s) in | Assessed | SMN1 | survival of motor neuron 1, telomeric | gene with protein product | Ensembl: ENSG00000172062; Genatlas: SMN1; HGNC: 11117; OMIM: 600354; Reactome: Q16637; SwissProt: Q16637; ClinVar: SMN1 | 20301526[PMID] |
| 83419 | http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=83419 | Proximal spinal muscular atrophy type 3 | Clinical subtype | Subtype of disorder | Disease-causing germline mutation(s) in | Assessed | SMN1 | survival of motor neuron 1, telomeric | gene with protein product | Ensembl: ENSG00000172062; Genatlas: SMN1; HGNC: 11117; OMIM: 600354; Reactome: Q16637; SwissProt: Q16637; ClinVar: SMN1 | 20301526[PMID] |
| 83420 | http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=83420 | Proximal spinal muscular atrophy type 4 | Clinical subtype | Subtype of disorder | Disease-causing germline mutation(s) in | Assessed | SMN1 | survival of motor neuron 1, telomeric | gene with protein product | Ensembl: ENSG00000172062; Genatlas: SMN1; HGNC: 11117; OMIM: 600354; Reactome: Q16637; SwissProt: Q16637; ClinVar: SMN1 | 20301526[PMID] |
| 83418 | http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=83418 | Proximal spinal muscular atrophy type 2 | Clinical subtype | Subtype of disorder | Disease-causing germline mutation(s) in | Assessed | SMN1 | survival of motor neuron 1, telomeric | gene with protein product | Ensembl: ENSG00000172062; Genatlas: SMN1; HGNC: 11117; OMIM: 600354; Reactome: Q16637; SwissProt: Q16637; ClinVar: SMN1 | 20301526[PMID] |
The source_of_validation column contains the reference for the association. In this case, all four associations were described in GeneReviews.
The natural history dataset contains more information about the inheritance pattern and age of onset of each of these disorders. The orphacode is a unique disorder identifier and can be used for merging.
natural_history_df = orphanet.natural_history()
smn1_natural_history = pd.merge(smn1_disorders[['orphacode', 'disorder_name']], natural_history_df, how='left', validate='1:1')
smn1_natural_history
| orphacode | disorder_name | expert_link | disorder_type | disorder_group | average_age_of_onset | type_of_inheritance |
|---|---|---|---|---|---|---|
| 83330 | Proximal spinal muscular atrophy type 1 | http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=83330 | Clinical subtype | Subtype of disorder | Infancy; Neonatal | Autosomal recessive |
| 83419 | Proximal spinal muscular atrophy type 3 | http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=83419 | Clinical subtype | Subtype of disorder | Adolescent; Adult; Childhood; Infancy | Autosomal recessive |
| 83420 | Proximal spinal muscular atrophy type 4 | http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=83420 | Clinical subtype | Subtype of disorder | Adult | Autosomal recessive |
| 83418 | Proximal spinal muscular atrophy type 2 | http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=83418 | Clinical subtype | Subtype of disorder | Infancy | Autosomal recessive |
The spinal muscular atrophy subtypes are numbered by the age of onset, with type 1 manifesting in infancy and type 4 in adulthood. All four subtypes have autosomal recessive inheritance.
We can also get prevalence estimates for each by cross-referencing the prevalence dataset. A disorder may have multiple prevalence estimates, and each is represented by a row.
prevalence_df = orphanet.prevalence()
smn1_prevalence = pd.merge(smn1_disorders[['orphacode', 'disorder_name']], prevalence_df, how='left', validate='1:m')
smn1_prevalence
| orphacode | disorder_name | expert_link | disorder_type | disorder_group | prevalence_source | prevalence_type | prevalence_qualification | prevalence_class | prevalence_geographic | prevalence_validation_status |
|---|---|---|---|---|---|---|---|---|---|---|
| 83330 | Proximal spinal muscular atrophy type 1 | http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=83330 | Clinical subtype | Subtype of disorder | ORPHANET | Annual incidence | Value and class | 1-9 / 1 000 000 | Europe | Not yet validated |
| 83330 | Proximal spinal muscular atrophy type 1 | http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=83330 | Clinical subtype | Subtype of disorder | ORPHANET | Point prevalence | Class only | 1-9 / 100 000 | Europe | Not yet validated |
| 83419 | Proximal spinal muscular atrophy type 3 | http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=83419 | Clinical subtype | Subtype of disorder | 1483045[PMID] | Prevalence at birth | Value and class | 1-9 / 1 000 000 | Italy | Validated |
| 83419 | Proximal spinal muscular atrophy type 3 | http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=83419 | Clinical subtype | Subtype of disorder | 28676062[PMID]_ORPHANET | Point prevalence | Class only | 1-9 / 1 000 000 | Europe | Validated |
| 83420 | Proximal spinal muscular atrophy type 4 | http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=83420 | Clinical subtype | Subtype of disorder | ORPHANET | Annual incidence | Class only | Unknown | Europe | Validated |
| 83420 | Proximal spinal muscular atrophy type 4 | http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=83420 | Clinical subtype | Subtype of disorder | ORPHANET | Point prevalence | Class only | Unknown | Europe | Validated |
| 83418 | Proximal spinal muscular atrophy type 2 | http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=83418 | Clinical subtype | Subtype of disorder | 10677857[PMID]_1483045[PMID] | Prevalence at birth | Value and class | 1-9 / 100 000 | Europe | Validated |
| 83418 | Proximal spinal muscular atrophy type 2 | http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=83418 | Clinical subtype | Subtype of disorder | 28676062[PMID]_ORPHANET | Point prevalence | Class only | 1-9 / 100 000 | Worldwide | Validated |
There are different types of prevalence estimates, as indicated by the prevalence_type column.
phenotypes = orphanet.associated_phenotypes()
smn1_phenotypes = pd.merge(smn1_disorders[['orphacode', 'disorder_name']], phenotypes, how='left', validate='1:m')
The functional consequences data contains information on clinician-reported consequences of the disease.
func_consequences = orphanet.functional_consequences()
smn1_func_consequences = pd.merge(smn1_disorders[['orphacode', 'disorder_name']], func_consequences, how='inner', validate='1:m')
| orphacode | disorder_name | expert_link | disorder_type | disorder_group | disability | frequence_disability | temporality_disability | severity_disability | loss_of_ability | type | defined | source_of_validation | specific_management | online | annotation_date | status_disability | disability_category |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 83419 | Proximal spinal muscular atrophy type 3 | http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=83419 | Clinical subtype | Subtype of disorder | Learning to write | Occasional | Acquisition delay | Low | n | Disability | y | Dr Emmanuelle SALORT CAMPANA[Expert] | n | y | 2022-11-01 00:00:00.0 | Not validated | Activity limitation/participation restriction |
| 83419 | Proximal spinal muscular atrophy type 3 | http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=83419 | Clinical subtype | Subtype of disorder | Learning to write | Occasional | Permanent limitation | Low | y | Disability | y | Dr Emmanuelle SALORT CAMPANA[Expert] | n | y | 2022-11-01 00:00:00.0 | Not validated | Activity limitation/participation restriction |
| 83419 | Proximal spinal muscular atrophy type 3 | http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=83419 | Clinical subtype | Subtype of disorder | Writing | y | Disability | n | Dr Emmanuelle SALORT CAMPANA[Expert] | n | y | 2022-11-01 00:00:00.0 | Not validated | Activity limitation/participation restriction | |||
| 83419 | Proximal spinal muscular atrophy type 3 | http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=83419 | Clinical subtype | Subtype of disorder | Speaking | Occasional | Permanent limitation | Low | y | Disability | y | Dr Emmanuelle SALORT CAMPANA[Expert] | n | y | 2022-11-01 00:00:00.0 | Not validated | Activity limitation/participation restriction |
| 83419 | Proximal spinal muscular atrophy type 3 | http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=83419 | Clinical subtype | Subtype of disorder | Producing messages in sign language | y | Disability | n | Dr Emmanuelle SALORT CAMPANA[Expert] | n | y | 2022-11-01 00:00:00.0 | Not validated | Activity limitation/participation restriction | |||
| 83419 | Proximal spinal muscular atrophy type 3 | http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=83419 | Clinical subtype | Subtype of disorder | Producing nonverbal messages | y | Disability | n | Dr Emmanuelle SALORT CAMPANA[Expert] | n | y | 2022-11-01 00:00:00.0 | Not validated | Activity limitation/participation restriction | |||
| 83419 | Proximal spinal muscular atrophy type 3 | http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=83419 | Clinical subtype | Subtype of disorder | Writing messages | y | Disability | n | Dr Emmanuelle SALORT CAMPANA[Expert] | n | y | 2022-11-01 00:00:00.0 | Not validated | Activity limitation/participation restriction | |||
| 83419 | Proximal spinal muscular atrophy type 3 | http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=83419 | Clinical subtype | Subtype of disorder | Using communication devices | y | Disability | n | Dr Emmanuelle SALORT CAMPANA[Expert] | n | y | 2022-11-01 00:00:00.0 | Not validated | Activity limitation/participation restriction | |||
| 83419 | Proximal spinal muscular atrophy type 3 | http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=83419 | Clinical subtype | Subtype of disorder | Standing | y | Disability | n | Dr Emmanuelle SALORT CAMPANA[Expert] | n | y | 2022-11-01 00:00:00.0 | Not validated | Activity limitation/participation restriction | |||
| 83419 | Proximal spinal muscular atrophy type 3 | http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=83419 | Clinical subtype | Subtype of disorder | Sitting | y | Disability | n | Dr Emmanuelle SALORT CAMPANA[Expert] | n | y | 2022-11-01 00:00:00.0 | Not validated | Activity limitation/participation restriction |