Orphadata provides the scientific community with comprehensive, massive, re-usable and computable quality data sets related to rare diseases from the Orphanet knowledge base, available through 4 distinct services:
* Files: Provided files are a partial extraction of the Orphanet knowledge base.
* APIs
* Customizable services
* Fair Datapoint
Provided by CARE AND TRIAL SITE REGISTRY FOR NEUROMUSCULAR AND NEURODEGENERATIVE DISEASES (CTSR)
Care and Trial Site Registry (CTSR) helps clinical investigators select trial sites as well as to help to identify potential partners for upcoming research projects.
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Services provided by EU-OPENSCREEN include
• assay adaption: This assay adaptation process will involve a strong emphasis on quality, including: quality control of reagents; (patho-)physiological relevance; pharmacological consistency; robustness; minimised variability; and tracking of statistical descriptors (e.g. signal to background and the Z’ factor)
• chemical optimization and profiling of preliminary ‘hits’
• bioprofiling of donated compounds: All compounds donated by the user which enter the EU-OPENSCREEN ERIC compound collection are characterised and annotated for basic physico-chemical (e.g. identity, solubility, light absorbance and fluorescence) and essential to know biological properties (cytotoxicity, antibiotic, antifungal etc.) by testing in a standard panel of assays.
• provision of standardised data: All data generated through QC/bioprofiling and screening activities will be published in EU-OPENSCREEN’s open-access database with an optional ‘grace’ period (i.e. delayed publication of data). Large-scale open-access data provide the basis for computational data integration to obtain a systematic view, allow for prediction of drug-target interactions and networks as well as of adverse effects and drug combinations. The access to the EU-OPENSCREEN database will utilize the facilities of ChEMBL.
Provided by EUROPEAN PLATFORM ON RARE DISEASE REGISTRATION (EU RD PLATFORM)
The European Rare Disease Registry Infrastructure (ERDRI) renders rare disease registries’ data searchable and findable. This is achieved through the provision of following components: European Directory of Registries (ERDRI.dor), Central Metadata Repository (ERDRI.mdr) and Pseudonymisation Tool.
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LOVD is a free, flexible web-based open source database designed to collect and display variants in the DNA sequence. LOVD offers free hosting and support of LOVD-powered gene variant databases
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The RD-Connect Registry & Biobank Finder is an online directory of existing rare disease databases, registries and biobanks.
The RD-Connect Registry & Biobank Finder lets researchers find the rare disease patient registries and biobanks that store data on their rare disease of interest. The system provides databases’ contact data and the numbers of registered cases for each disease in the registry/biobank, regularly updated by the database curators.
Users can search the directory by disease name and its synonyms, ORPHA- or OMIM-codes and other keywords, such as the country or registry manager. The system also provides access to documents such as databases’ study protocols, case report forms, informed consent templates and data access agreements.
Provided by DATABASE OF GENOMIC VARIATION AND PHENOTYPE IN HUMANS USING ENSEMBL RESOURCES (DECIPHER)
DECIPHER is a clinical and research tool used by the clinical community to share and compare phenotypic and genotypic data and to
1. Aid in the interpretation of data from genome-wide analyses e.g. the differentiation between pathogenic and benign genomic variants.
2. Utilise the human reference sequence via Ensembl and other genome browsers to define which genes are involved in a specific structural variant (e.g. copy number variant) and for smaller variants (e.g. sequence variants), whether they are positioned within a gene or regulatory element and predict their likely consequence.
3. Facilitate research into the study of genes that affect human health and development to define new gene-disease and variant-disease associations and to improve diagnosis, management and therapy of rare diseases.
Provided by EUROPEAN BIOINFORMATICS INSTITUTE (EBI)
EBI makes the world’s public biological data freely available to the scientific community via a range of services and tools and helps scientists everywhere turn information into knowledge in the following areas:
Genes, genomes & variation
Expression
Protein sequences
Molecular & cellular structures
Chemical biology
Pathways & systems
The goal of the ELIXIR Data Platform is to drive the use, re-use and value of life science data. It aims to do this by providing users with robust, long-term sustainable data resources within a coordinated, scalable and connected data ecosystem. Bioinformaticians and life science researchers in both academic and industrial settings need confidence in the sound governance, life cycle management, and long-term sustainability of those data resources.
Platform highlights
ELIXIR Core Data Resources: European data resources that are of fundamental importance to research in the life sciences and are committed to the long-term preservation of data.
ELIXIR Deposition Databases: repositories recommended for the deposition of life sciences experimental data.
Data resource services: this list is updated as Nodes finalise or review their Service Delivery Plans
The European COVID-19 Data Platform consists of three connected components:
1. SARS-CoV-2 Data Hubs, which organise the flow of SARS-CoV-2 outbreak sequence data and provide comprehensive open data sharing for the European and global research communities.
2. Federated European Genome-phenome Archive, which provides secure controlled access sharing of sensitive patient and research subject data sets relating to COVID-19.
3. COVID-19 Data Portal, which brings together and continuously update relevant COVID-19 datasets and tools, will host sequence data sharing and will facilitate access to other SARS-CoV-2 resources.
