UniProtDisease

Introduction

UniProt is a central database in life sciences capturing information about proteins. UniProt was one of the first databases to adopt SPARQL-based access through the UniProt SPARQL endpoint. It allows access to curated and automatically generated information about protens across all Kingdoms of life.

Relation types

The aim of this task is to predict protein-to-disease associations usually reflecting an involvement of a protein in a disease.

Data sources and contact

Data in UniProt can be explored using the UniProt website and the UniProt SPARQL endpoint.

Data download and evaluation

Dataset download: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/

Endpoint: https://sparql.uniprot.org/sparql/

Query for evaluation:

PREFIX keywords:<http://purl.uniprot.org/keywords/> 
PREFIX uniprotkb:<http://purl.uniprot.org/uniprot/> 
PREFIX taxon:<http://purl.uniprot.org/taxonomy/> 
PREFIX ec:<http://purl.uniprot.org/enzyme/> 
PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#> 
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> 
PREFIX skos:<http://www.w3.org/2004/02/skos/core#> 
PREFIX owl:<http://www.w3.org/2002/07/owl#> 
PREFIX bibo:<http://purl.org/ontology/bibo/> 
PREFIX dc:<http://purl.org/dc/terms/> 
PREFIX xsd:<http://www.w3.org/2001/XMLSchema#> 
PREFIX faldo:<http://biohackathon.org/resource/faldo#> 
PREFIX GO:<http://purl.obolibrary.org/obo/GO_> 
PREFIX allie:<http://allie.dbcls.jp/> 
PREFIX CHEBI:<http://purl.obolibrary.org/obo/CHEBI_> 
PREFIX cco:<http://rdf.ebi.ac.uk/terms/chembl#> 
PREFIX codoa:<http://purl.glycoinfo.org/ontology/codao#> 
PREFIX ensembl:<http://rdf.ebi.ac.uk/resource/ensembl/> 
PREFIX ensemblexon:<http://rdf.ebi.ac.uk/resource/ensembl.exon/> 
PREFIX ensemblprotein:<http://rdf.ebi.ac.uk/resource/ensembl.protein/> 
PREFIX ensemblterms:<http://rdf.ebi.ac.uk/terms/ensembl/> 
PREFIX ensembltranscript:<http://rdf.ebi.ac.uk/resource/ensembl.transcript/> 
PREFIX glycan:<http://purl.jp/bio/12/glyco/glycan#> 
PREFIX glyconnect:<https://purl.org/glyconnect/> 
PREFIX identifiers:<http://identifiers.org/> 
PREFIX mesh:<http://id.nlm.nih.gov/mesh/> 
PREFIX mnet:<https://rdf.metanetx.org/mnet/> 
PREFIX mnx:<https://rdf.metanetx.org/schema/> 
PREFIX orthodb:<http://purl.orthodb.org/> 
PREFIX orthodbGroup:<http://purl.orthodb.org/odbgroup/> 
PREFIX patent:<http://data.epo.org/linked-data/def/patent/> 
PREFIX pubmed:<http://rdf.ncbi.nlm.nih.gov/pubmed/> 
PREFIX rh:<http://rdf.rhea-db.org/> 
PREFIX schema:<http://schema.org/> 
PREFIX sh:<http://www.w3.org/ns/shacl#> 
PREFIX sio:<http://semanticscience.org/resource/> 
PREFIX slm:<https://swisslipids.org/rdf/> 
PREFIX sp:<http://spinrdf.org/sp#> 
PREFIX uberon:<http://purl.obolibrary.org/obo/uo#> 
PREFIX up:<http://purl.uniprot.org/core/> 
SELECT ?prot ?val
WHERE
{

        ?prot up:annotation ?o .
  		?o a up:Disease_Annotation .
  		?o up:disease ?val .
  	[] rdf:subject ?o ;
                   rdf:predicate up:disease ;
                   rdf:object ?val ;
                   up:attribution /up:evidence ?eco .
	FILTER (?eco IN (<http://purl.obolibrary.org/obo/ECO_0000269>, <http://purl.obolibrary.org/obo/ECO_0000303>, <http://purl.obolibrary.org/obo/ECO_0000305>) ) .
}

Rankings

Ranking

New submission

To submit, create a compressed (gzip or zip) tab-separated file containing (subject, predicate, object, score) quadruples. An example file could be:

<https://reactome.org/content/detail/R-HSA-2172127> <http://purl.obolibrary.org/obo/RO_0000057> <http://www.ncbi.nlm.nih.gov/gene/5710> 0.9
<http://purl.obolibrary.org/obo/CHEBI_4034> <http://purl.obolibrary.org/obo/RO_0002434> <https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000546491> 0.1
<http://purl.obolibrary.org/obo/CHEBI_49662> <http://purl.obolibrary.org/obo/RO_0002434> <https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000344604> 0.231
<http://purl.obolibrary.org/obo/PR_P63010> <http://purl.obolibrary.org/obo/RO_0002436> <http://purl.obolibrary.org/obo/PR_P51812> 0.111
<http://purl.obolibrary.org/obo/MONDO_0009452> <http://purl.obolibrary.org/obo/RO_0002200> <http://purl.obolibrary.org/obo/HP_0001290> 0
<http://purl.obolibrary.org/obo/CHEBI_46195> <http://purl.obolibrary.org/obo/RO_0002434> <https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000546299> 1.0
<http://purl.obolibrary.org/obo/PR_Q8ND25> <http://purl.obolibrary.org/obo/RO_0002512> <https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000320619> 0.4291
<http://www.ncbi.nlm.nih.gov/gene/2065> <http://purl.obolibrary.org/obo/RO_0002559> <https://www.ncbi.nlm.nih.gov/snp/rs115311663> 0.1
<http://purl.obolibrary.org/obo/PR_Q13480-2> <http://purl.obolibrary.org/obo/RO_0002436> <http://purl.obolibrary.org/obo/PR_P16333-1> 0.5
<http://purl.obolibrary.org/obo/CHEBI_78802> <http://purl.obolibrary.org/obo/RO_0002436> <http://purl.obolibrary.org/obo/GO_0006875> 0
	

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