Datasets

GGDonto

Website

GGDonto is the Ontology of the Genetic Diseases related to the Glycan Metabolism. GGDonto describes the knowledge about Congenital Disorders of Glycosylation (CDG) and Lysosomal Storage Diseases (LSD). GGDonto provides the information on 120 genetic diseases of the glycan synthesis and the degradation and their causative genes.

Dataset specifications

Tags
Other biomolecule Health/Disease Gene Ontology/Terminology/Nomenclature Interaction/Pathway
Provenance Original
Registration Submitted
Data provider
  • Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST)
Creator
  • Hisashi NarimatsuGlycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST)
  • Toshihide ShikanaiGlycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST)
  • Elena SolovievaGlycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST)
  • Noriaki FujitaGlycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST)
Issued 2017-01-25
Licenses
  • Attribution-NonCommercial-ShareAlike 2.1 Japan (CC BY-NC-SA 2.1)
Version v.1.0
Download /download/#ggdonto
SPARQL Endpoint https://rdfportal.org/primary/sparql

Dataset statistics

Triples
39523
Subjects
1783
Properties
918
Objects
9083
Classes
20

SPARQL example queries

Example 1

Run on Endpoint 
### List the preferred names and synonyms for diseases which are the Congenital Disorders of Glycosylation ###
prefix ggdsch: <http://jcggdb.jp/rdf/diseases/ggdonto-schema#>

select distinct ?preferred_name ?synonym
from <http://jcggdb.jp/rdf/diseases/ggdonto>
where {
 ?disease_uri a ggdsch:DiseaseDescriptionGGDonto .
 ?disease_uri ggdsch:diseaseType ggdsch:CDG .
 ?disease_uri ggdsch:diseasePreferredTerm ?preferred_name.
 OPTIONAL {
  ?disease_uri ggdsch:diseasePreferredTerm ?preferred_name.
  ?disease_uri ggdsch:diseaseSynonyms ?synonym.
  FILTER ( lang(?preferred_name) = lang(?synonym) )
 }
}
order by ?preferred_name ?synonym

Example 2

Run on Endpoint 
### Get the symptoms of a disease for which the UMLS CUI (Concept Unique Identifier from Unified Medical Language System) is 'C2931008' ###
prefix skos: <http://www.w3.org/2004/02/skos/core#>
prefix ggdsch: <http://jcggdb.jp/rdf/diseases/ggdonto-schema#>
prefix gmsch: <http://jcggdb.jp/rdf/diseases/gmncbi-schema#>

select distinct ?manifestation 
from <http://jcggdb.jp/rdf/diseases/ggdonto>
where {
 ?disease_uri a ggdsch:DiseaseDescriptionGGDonto .
 ?disease_uri ggdsch:umlsCUI "C2931008".
?disease_uri gmsch:hasManifestation ?manifestation_uri .
 ?manifestation_uri skos:prefLabel ?manifestation .
}

Example 3

Run on Endpoint 
### Get the references for a disease which has the name or aliases like 'CDG-IIa' ###
prefix skos: <http://www.w3.org/2004/02/skos/core#>
prefix ggdsch: <http://jcggdb.jp/rdf/diseases/ggdonto-schema#>

select distinct ?reference
from <http://jcggdb.jp/rdf/diseases/ggdonto>
where {
 ?disease_uri a ggdsch:DiseaseDescriptionGGDonto.
 {?disease_uri skos:prefLabel  "CDG-IIa"@en.}
 UNION
 {?disease_uri skos:altLabel "CDG-IIa"@en.}
 ?disease_uri ggdsch:referencesInfo ?reference.
}

Schema diagram

Schema diagram for ggdonto
Schema diagram for ggdonto