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Orphadata: Aggregated Data From Orphanet   (All Phenotype and Literature tracks)

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Data last updated at UCSC: 2021-11-04 11:49:58

Description

NOTE:
These data are for research purposes only. While the Orphadata data is open to the public, users seeking information about a personal medical or genetic condition are urged to consult with a qualified physician for diagnosis and for answers to personal medical questions.

UCSC presents these data for use by qualified professionals, and even such professionals should use caution in interpreting the significance of information found here. No single data point should be taken at face value and such data should always be used in conjunction with as much corroborating data as possible. No treatment protocols should be developed or patient advice given on the basis of these data without careful consideration of all possible sources of information.

No attempt to identify individual patients should be undertaken. No one is authorized to attempt to identify patients by any means.

The Orphadata: Aggregated data from Orphanet (Orphanet) track shows genomic positions of genes and their association to human disorders, related epidemiological data, and phenotypic annotations. As a consortium of 40 countries throughout the world, Orphanet gathers and improves knowledge regarding rare diseases and maintains the Orphanet rare disease nomenclature (ORPHAcode), essential in improving the visibility of rare diseases in health and research information systems. The data is updated monthly by Orphanet and updated monthly on the UCSC Genome Browser.

Display Conventions

Mouseover on items shows the gene name, disorder name, modes of inheritance(s) (if available), and age(s) of onset (if available). Tracks can be filtered according to gene-disorder association types, modes of inheritance, and ages of onset. Clicking an item from the browser will return the complete entry, including gene linkouts to Ensembl, OMIM, and HGNC, as well as phenotype information using HPO (human phenotype ontology) terms. For more information on the use of this data, see the Orphadata FAQs.

Data Access

The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.

Data is also freely available through Orphadata datasets.

Methods

Orphadata files were reformatted at UCSC to the bigBed format.

Credits

Thank you to the Orphanet and Orphadata team and to Tiana Pereira, Christopher Lee, Daniel Schmelter, and Anna Benet-Pages of the Genome Browser team.

References

Pavan S, Rommel K, Mateo Marquina ME, Höhn S, Lanneau V, Rath A. Clinical Practice Guidelines for Rare Diseases: The Orphanet Database. PLoS One. 2017;12(1):e0170365. PMID: 28099516; PMC: PMC5242437

Nguengang Wakap S, Lambert DM, Olry A, Rodwell C, Gueydan C, Lanneau V, Murphy D, Le Cam Y, Rath A. Estimating cumulative point prevalence of rare diseases: analysis of the Orphanet database. Eur J Hum Genet. 2020 Feb;28(2):165-173. PMID: 31527858; PMC: PMC6974615