Table 3 Overview of selected RDF resources in the domain of rare diseases
From: Assessing resolvability, parsability, and consistency of RDF resources: a use case in rare diseases
Resource | Description | Version | Link |
|---|---|---|---|
rare-disease biobanks and registries | Metadataset providing a list of biobanks and patient registries in the EJP RD. | 2021/9/30 | |
Head and neck tumor registry Austria | Metadata of a single patient registry. | 2021/9/30 | |
A biobank of patients with Primary Immune Deficiencies | Metadata of a single biobank. | 2021/9/30 | |
NeXtProt schema | A schema describing the structures of NeXtProt data. | 2022/6/28 | https://download.nextprot.org/pub/current_release/rdf/ttl/schema.ttl.gz |
Orphanet catalog schema | A schema describing the ontological structure of proof-of-concept FAIR Data Point for biobank and patient registry in the EJP RD. | 2022/6/14 | |
hPSCreg vocabulary | A collection of terms used in the registry for human pluripotent stem cell lines ( hPSC lines). | 2022/7/26 | |
Resource Metadata Ontology | A collection of terms used in the EJP RD metadatasets. | v 1.0 | |
The WikiPathways Ontology | Ontology defining the classes and properties used in the WikiPathways - a collaborative platform for the creation and maintenance of content related to biological pathways. | 2022/7/11 | |
NeXtProt vocabulary | Ontology defining all the classes and properties used in the NeXProt - an online knowledge platform on human proteins. | 2022/6/28 | https://download.nextprot.org/pub/current_release/rdf/ttl/terminology.ttl.gz |
UniProt ontology | A collection of terms used to describe the entries and associated data in UniProt, which is the database of protein sequence and functional information. | 2022/3/1 | |
Orphanet Rare Disease Ontology (ORDO) | ‘A structured vocabulary for rare diseases derived from the Orphanet database, capturing relationships between diseases, genes and other relevant features.’ | 2022/12/6 | |
Anatomical Therapeutic Chemical Classification (ATC) | ‘a classification of active ingredients of drugs according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties.’ | 2022/5/2 | |
Human Phenotype Ontology (HPO) | ‘a standardized vocabulary of phenotypic abnormalities encountered in human disease.’ | 2022/10/5 | http://purl.obolibrary.org/obo/hp/releases/2022-10-05/hp.owl |
Gene Ontology (GO) | A knowledge base providing the information on the functions of genes. | 2022/8/10 | |
SNOMED CT | ‘It is the most comprehensive, multilingual, clinical healthcare terminology in the world and is a resource with scientifically validated clinical content that is released monthly.’ | 2020/3/11 | Not available. License is needed. |
National Cancer Institute Thesaurus (NCIT) | ‘It is a widely recognized standard for biomedical coding and reference, used by a broad variety of public and private partners both nationally and internationally’ | 01/05/2023 |