Users may download the datasets made available on www.orphadata.com in the Orphadata Science section and use them as they wish (including use in other information systems) according to the Commons Attribution 4.0 International (CC BY 4.0) licence that we have decided to apply to Orphadata Science datasets and APIs. This means that you are free to copy, distribute, display and make commercial use of this data in all legislations, provided you give us credit (citation guidelines below).
You must indicate if you have made changes to the data. This can be done so in a reasonable manner, but not in any way that suggests that Orphanet endorses you or your use.
You may not apply legal terms or technological measures that legally restrict others from doing anything the licence permits ( please consult the terms of licence for more information).
When this licence is applied, it is stated clearly on the page giving access to the dataset and in the dataset itself.
If you have any doubts on the use you wish to make of this data, please contact us.
Use of datasets in the catalogue of Expert Resources is subject to the terms of a Data Transfer Agreement, or a Service Contrat (depending on the user’s status), to be signed before access to the files is granted. Please contact us for more information.
The appropriate form when quoting Orphanet is:
Orphanet: an online rare disease and orphan drug data base. © INSERM 1999. Available on http://www.orpha.net. Accessed (date accessed).
The appropriate form when quoting Orphadata is:
Orphadata: Free access data from Orphanet. © INSERM 1999. Available on https://www.orphadata.com. Data version (XML data version).
Use of our logos is subject to our prior approval. Please use the contact form to ask.
We have described our freely accessible datasets, request datasets, ORDO and HOOM in a series of documents, below. These documents also include annotated samples of the data, and schemas when applicable: free products description, on request products description, ORDO and HOOM.
If you have to ask, you are probably not at ease with parsing and processing XML. Extensible Markup Language (XML) is a markup language that defines a set of rules for encoding documents in a format that is both human-readable and machine-readable.See Wikipedia for further information.But, don’t worry, it is still possible to use the data in a simple way. There is plenty of software able to open it. For instance, if you are an Excel user, it is very easy: just download a file (right-click the link and download it). Once it is downloaded, just open it with a recent version of Excel (2003 or later). Excel will transform the XML into a wonderful Excel spreadsheet. Then you can save it in any other format convenient for you (xls, cvs, txt etc.)Mac users, beware! It seems that Office on Mac OS version has some difficulties managing XML in general.
The data on the Orphanet website is managed daily. For more information, see the PDF to understand how are the data produced.
Also, in Orphadata the dataset is a partial extraction of the data stored in Orphanet, which is also accessible at www.orpha.net for consultation purposes only. For instance in Orphanet you may find some diseases which are not rare (or rare in USA but not in Europe) while in Orphadata you will not find a non rare disease.
The XML files freely available on this website are produced twice a year in June and in December.
The Orphanet nomenclature of Rare diseases (ORPHAcodes) is organised in a classification system with groups (organising the medical domains), disorders, and subtypes (if relevant). Genes are associated to ORPHAcodes as precisely as possible in the classification system: this means at the subtype level if it exists otherwise at the disorder level. On the Orphanet website, genes are displayed where they have been linked, but also at upper levels: if a gene is associated to a subtype, then the disorder level (parent of the subtype in the classification) inherited this gene: the gene is also displayed at the disorder level.
Example:
ORPHA:93581 Orphanet: Atypical hemolytic uremic syndrome with anti factor H antibodies (Subtype of disorder) is associated to CHFR1, CHFR3, CHFR5 and CHFR6 AND ORPHA:544472 Orphanet: Atypical hemolytic uremic syndrome with complement gene abnormality (Subtype of disorder) is associated to CD46, CFH, CFI, THBD, CFB and C3.
This information is available in here in the Orphadata gene product (product 6) and on the Orphanet website. However, ORPHA:2134 Atypical hemolytic uremic syndrome (Disorder), parent of both subtypes, is absent of product 6. On the website, 10 genes are displayed (Orphanet: Atypical hemolytic uremic syndrome) because “inherited” from its subtypes through the classification.
In order to build this information, you need to use the product6 and the classification product product3_156 (the rare genetic diseases classification).
So, inclusion in product 6 is only a technical choice and not associated to a level of evidence of the gene to disease relationship.
Yes, it is possible, please contact us.
We are open to exploring partnerships. You can contact us using our contact form. I’m a student /patient/professional. I would like to ask you something about a rare disease, or for a specific case which is not related to Orphadata dataset itself.
Yes, you can, please contact us.
Yes, this is possible. Just ask using our contact form.
Some extensions for browsers (if locally installed) let you to display XML by opening the file in a new tab/window. We would advise Pretty XML or XML Viewer Plus for Firefox or Google Chrome
You can find additional information in our legal notice.
If you have any other questions, please contact us.
