Orphanet

Annual visits:
13 209 809 an
Unique visits:
9 139 373 an
Quotes:
2 680
Latest update:
18-01-2017

Orphanet

Description
Information portal on rare diseases and orphan drugs: http://www.orpha.net
Access conditions

Freely accessible.

Annual visits:
50 000 an
Unique visits:
10 468 an
Quotes:
45
Latest update:
02-01-2017

Orphadata

Description
Datasets from the Orphanet database made available in XML format and in OWL format for the Orphanet Rare Disease Ontology, via  www.orphadata.org
Access conditions
Freely accessible for public data (rare disease nomenclature and disease-gene relationships); other data acessible via a Data Transfert Agreement and annual licence fee (free for academic collaborations)  for data related to activities in the field of rare diseases (inventory of rare disease research projects, clinical trials, expert centres, patient organisations, and data on epidemiology, orphan drugs, encyclopaedia).
Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
39
Downloads:
6 741

ORDO

Description
Orphanet Rare Disease Ontology: Nomenclature, classifications and scientific data on rare diseases exploitable in an ontological form in OWL format. Elaborated in partnership with the European Bioinformatics Institute (EBI ; Contact Helen Parkinson). Available since January 2014.
Access conditions
Downloadable and freely accessible via Orphadata.org,

Downloadable and usable via Bioportal.

Availability of a sparql EndPoint.

Domains of activity
  • Biomedical
Description of expertise domains

Orphanet has particular expertise in the field of rare diseases, in particular the clinical and medical aspects of these diseases (natural history, diagnosis and care), their epidemiology (prevalence, incidence, prevalence at birth, geographical distribution, and age of onset and death), their genetic basis (genetic determinants of causalité/susceptibility), their phenotypic aspect (frequence of the occurance of different phenotypic traits), their nosology (via a multi-dimensional classification), and terminologies of these diseases (for semantic interoperability). Orphanet's coverage of the domain is also geographical, as Orphanet gives access to information concerning the expertise associated with rare diseases, the diagnostic offer, and the state of the art of research in around 40 countries.

Orphanet provides data and services with a high level of added-value as the data presented are integrated with other data and databases, qualified, expert-validated and quality controlled.
 

Keywords:
  • Machine learning
  • Integration of heterogeneous data
  • Knowledge representation
  • Ontologies
  • Semantic Web
  • Data curation
  • Information and communication technology developments
  • Tools
  • Interoperability
  • Interfaces, web portals
  • Data
  • Data integration
  • Databases and information systems
Users distribution
International
75 %
National
25 %
Regional
10 %
Local
1%
Explanation about this distribution:

In terms of the data accessed via the Orphanet website 1,83% of sessions come from the  APHP network (one session can equal multiple users). 12%  of sesions are regional (île de France) and 33,77% of the total number of sessions are nationals (this includes local and regional users). These figures cover the period 1 January 2015 to 20 October 2015.

In terms of the consultation of Orphadata, 0,41% of sessions come from the APHP, 8,2% of sessions are regional (île de France) and 15,60%  of the total number of sessions are national. These figures cover the period 1 January 2015 to 20 October 2015.

Platform's own projects

Not Documented

Collaborations
National projets
(1)
  • Coordinator of the eRare ERA-NET  project “HIPBI-RD - Harmonising phenomics information for a better interoperability in the RD field” 2016- 2018. Financed by the ANR for the French team.
International and European projects
(5)
  • Coordinator of the Joint Action RD-ACTION (DG Santé) 2015-2018 : a Joint Action bridging rare disease data and the elaboration of rare disease policies in Europe, co-financed by the European Commission and EU Member States
  • Coordinator of the eRare ERA-NET  project “HIPBI-RD - Harmonising phenomics information for a better interoperability in the RD field” 2016- 2018. Financed by the ANR for the French team.
  • Coordinator of the FP7 Project “Support IRDIRC” (2012-2018), supporting the scientific secretariat of the International Rare Disease Research Consortium.
  • Participation in other European projects such as RD-Connect, Joint Action on Rare Cancers, and ELIXIR-EXCELERATE as data providers/curators and interoperability vector.
Projets with industry
(1)

Improvement of the database, with the support of GSK (ended in 2015).

Collaboration projects not founded through an external organism
(2)
  • Collaboration with the International Health Terminology Standards Development Organisation so as to include rare diseases in SNOMED-CT and align Orphanet -SNOMED-CT.
  • Collaboration with NCATS-NIH (Genetic and Rare Disease Information Center) to align the nomenclatures and improve information provision.

 

Provision of services not founded through an external organism
Not documented
Animations (Workshops, Work-groups, seminars, conferences ... )

Working groups of the « European Commission Expert Group on Rare Diseases » concerning the codification of rare diseases in health information systems.

  1. Workshop on cross-referencing of terminologies, 27-28 September 2012, Paris
  2. Validation workshop on International Consortium of Human Phenotype Terminology terms, Boston on 21-22 October 2013
  3. Workshop on Orpha codes in health information systems, 18 March 2014, Paris
  4. Workshop on Orpha codes in health information systems, 1-2 October 2014, Ispra
  5. Workshop « Clinical trials for rare diseases : Exploring synergies between ECRIN and Orphanet networks ». Paris, 27 October 2015 – ICM Pitié Salpêtrière.
Internal publications

Orphanet: a database of genes with clinical significance in rare diseases
C. Gonthier, A. Olry, S. Janmaat, M. Hanauer, S. Gérard, A. Rath, European Society of Human Genetics Meeting, June 2015, Glasgow, UK


Rare diseases and disabilities: An Orphanet project to improve the information currently available
De Chalendar Myriam, Daniel Marie, Bee Stephanie, Olry Annie, Gerard Sylvain, Urbero Bruno, Lanneau Valérie, Rath Ana, WHO-FIC Meeting, October 2015, Manchester, UK


Orphanet services to the research community
V.Hivert, A.Rath, A Olry, C. Gonthier, N. Marpillat, M-P. Bécas-Garro, S. Peixoto, B. Belloir, C. Gueydan, M. Hanauer, B. Urbero, S. Aymé
ECRD 2014 9-11 May 2014, Berlin, Germany


Needs for Information on rare diseases: the most used Orphanet services and products as an indicator
S.Maiella, A.Rath, M.Hanauer, B.Urbero, J.Christ & S.Aymé
ECRD 2014 9-11 May 2014, Berlin, Germany


German data collection of expert services for rare diseases in Orphanet database: state of the art 2013
Mareike Derks, Kathrin Rommel, Elisabeth Nyoungui, Joerg Schmidtke
ECRD 2014 9-11 May 2014, Berlin, Germany


A survey on the centres of expertise for rare diseases in Italy
R. Mingarelli, S. Ciampa, R. Ruotolo, M. Di Giacinto, S. Festa, E. Cocchiara, B. Dallapiccola
ECRD 2014 9-11 May 2014, Berlin, Germany


Rare diseases and disabilities: 3 Orphanet projects to improve the information currently available
M. de Chalendar, D. Marie, S.Bee, J-S. Giraudet, A. Olry, J. Christ, A. Rath
ICORD 2014, Ede, The Netherlands, 7-9 October


Dissemination of good quality clinical practice guidelines for rare diseases through the Orphanet website
Pavan Sonia, Jaramillo Clara, Christ Julie, Rath Ana
ICORD 2014 Ede, The Netherlands, 7-9 October[Orphanet and its consortium: where to find expert-validated information on rare diseases]. Maiella S, Rath A, Angin C, Mousson F, Kremp O, [Article in French].Rev Neurol (Paris). 2013 Feb;169 Suppl 1:S3-8. doi: 10.1016/S0035-3787(13)70052-3.


Orphanet, The reference portal of over 6,000 rare diseases, including all genetic diseases, European Society of Human Genetics Conference, June 2013, Paris

External publications

Annotating rare diseases with HPO terms : a new Orphanet service to refine phenotype-genotype correlations.
Olry A, Prévot C., Jaramillo C., Gonthier C. Janmaat S., Lanneau V., Gérard S., Hanauer M., Robinson PN., Rath A., American Society of Human Genetics Meeting 2015, 5-10 October Baltimore, USA


The Orphanet Rare Disease Ontology (ORDO): data modelling for rare diseases and genes
Annie Olry, Drashtti Vasant, James Malone, Catherine Gonthier, Sivakami Arunachalam, Marc Hanauer, Helen Parkinson, Ana Rath, European Society of Human Genetics Meeting 2015, Glasgow, UK


Annotating rare diseases with HPO terms : a new Orphanet service to refine phenotype-genotype correlations.

Olry A, Prévot C., Jaramillo C., Gonthier C. Janmaat S., Lanneau V., Gérard S., Hanauer M., Robinson PN., Rath A., Phenotype Day 2015


ORDO: An Ontology Connecting Rare Disease, Epidemiology and Genetic Data,
Drashtti Vasant, Laetitia Chanas, James Malone, Marc Hanauer, Annie Olry, Simon Jupp, Peter N. Robinson, Helen Parkinson, and Ana Rath, Phenotype Day 2014.


The Orphanet Rare Diseases Ontology (ORDO) : A Reference Tool Integrating Clinical and Genetic Data
A Rath, A . Olry, C. Gonthier, L. Chanas, H. Parkinson, J. Malone, D. Vasant, M. Hanauer, B. Urbero, S. Ayme
Annual Meeting of the American Society of Human Genetics, San Diego, USA, 19th-22nd October 2014


Phenotype terminologies in use for genotype-phenotype databases: A common core for standardisation and interoperability.
P.N. Robinson, S. Aymé, L. Chanas, A. Hamosh, A. Rath
Annual Meeting of the American Society of Human Genetics, San Diego, USA, 19th-22nd October 2014


The Orphanet Rare Diseases Ontology (ORDO): a reference tool integrating clinical and genetic data
Rath, A. Olry, C. Gonthier, L. Chanas, H. Parkinson, J.Malone, D. Vasant, M. Hanauer, B. Urbero, S. Aymé
ECRD 2014 9-11 May 2014, Berlin, Germany


Rare diseases ontology: a tool integrating clinical and genetics data for the researchers
A. Rath, A. Olry, C. Gonthier, L. Chanas, H. Parkinson, D. Vasant, J. Malone, M. Hanauer, B. Urbero and S.Aymé.
7ème assises de génétique humaine et médicale, Bordeaux, 29-31 janvier 2014


Dispelling myths about rare disease registry system development,
Matthew Bellgard, Christophe Beroud, Kay Parkinson, Tess Harris, Segolene Ayme, Gareth Baynam, Tarun Weeramanthri, Hugh Dawkins and Adam Hunter, Source Code for Biology and Medicine, 2013, 8:21


Rare diseases and now rare data?, Deborah Mascalzoni, Bartha Maria Knoppers, Ségolène Aymé, Matteo Macilotti, Hugh Dawkins, Simon Woods & Mats G. Hansson, Nature Reviews Genetics 14, 372 (2013)


EURO-WABB: an EU rare diseases registry for Wolfram syndrome, Alström syndrome and Bardet-Biedl syndrome, Amy Farmer, Ségolène Aymé, Miguel Lopez de Heredia, Pietro Maffei, Susan McCafferty, Wojciech Młynarski, Virginia Nunes, Kay Parkinson, Véronique Paquis-Flucklinger, Julia Rohayem, Richard Sinnott, Vallo Tillmann, Lisbeth Tranebjærg and Timothy G Barrett, BMC Pediatrics 2013, 13:130

Publications with the hosting laboratory
Acknowledgement

39 papers have cited Orphanet Rare Disease Ontology as a source of information/tool. 99 papers have cited Orphadata as a source of information.

Development

Orphanet is a trademark registered by the INSERM.

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