DeepGOWeb SPARQL Endpoint

The SPARQL endpoint allows to call function prediction model in SPARQL query. We provide a custom function called "deepgo" which takes protein sequence and prediction threshold as an input and returns predicted functions along with the subontology, label and prediction score. The output can be downloaded in different formats such as json, xml, csv or text.

Example queries:

• Example 1: Simple example query
• Example 2: Federated query which runs deepgo on two sequences from UniProt SPARQL Endpoint

PREFIX dg: <http://deepgoplus.bio2vec.net/functions#> PREFIX GO: <http://purl.obolibrary.org/obo/GO_> SELECT ?ont ?go ?label ?score { (?ont ?go ?label ?score) dg:deepgo("MPYKLKKEKEPPKVAKCTAKPSSSGKDGGGENTEEAQPQPQPQPQPQAQSQPPSSNKRPSNSTPPPTQLSKIKYSGGPQIVKKERRQSSSRFNLSKNRELQKLPALKDSPTQEREELFIQKLRQCCVLFDFVSDPLSDLKFKEVKRAGLNEMVEYITHSRDVVTEAIYPEAVTMFSVNLFRTLPPSSNPTGAEFDPEEDEPTLEAAWPHLQLVYEFFLRFLESPDFQPNIAKKYIDQKFVLALLDLFDSEDPRERDFLKTILHRIYGKFLGLRAYIRRQINHIFYRFIYETEHHNGIAELLEILGSIINGFALPLKEEHKMFLIRVLLPLHKVKSLSVYHPQLAYCVVQFLEKESSLTEPVIVGLLKFWPKTHSPKEVMFLNELEEILDVIEPSEFSKVMEPLFRQLAKCVSSPHFQVAERALYYWNNEYIMSLISDNAARVLPIMFPALYRNSKSHWNKTIHGLIYNALKLFMEMNQKLFDDCTQQYKAEKQKGRFRMKEREEMWQKIEELARLNPQYPMFRAPPPLPPVYSMETETPTAEDIQLLKRTVETEAVQMLKDIKKEKVLLRRKSELPQDVYTIKALEAHKRAEEFLTASQEAL" 0.3) . } PREFIX dg: <http://deepgoplus.bio2vec.net/functions#> PREFIX GO: <http://purl.obolibrary.org/obo/GO_> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?protein ?organism ?isoform ?sub ?go ?label ?score WHERE { { SELECT DISTINCT ?protein ?organism ?isoform ?aa_sequence WHERE { SERVICE <http://sparql.uniprot.org/sparql> { ?protein a up:Protein . ?protein up:organism ?organism . ?organism rdfs:subClassOf taxon:9606 . ?protein up:sequence ?isoform . ?isoform rdf:value ?aa_sequence . } } LIMIT 2 } (?sub ?go ?label ?score) dg:deepgo(?aa_sequence 0.3) . }

SPARQL Query

PREFIX dg: <http://deepgoplus.bio2vec.net/functions#> PREFIX GO: <http://purl.obolibrary.org/obo/GO_> SELECT ?ont ?go ?label ?score { (?ont ?go ?label ?score) dg:deepgo("MPYKLKKEKEPPKVAKCTAKPSSSGKDGGGENTEEAQPQPQPQPQPQAQSQPPSSNKRPSNSTPPPTQLSKIKYSGGPQIVKKERRQSSSRFNLSKNRELQKLPALKDSPTQEREELFIQKLRQCCVLFDFVSDPLSDLKFKEVKRAGLNEMVEYITHSRDVVTEAIYPEAVTMFSVNLFRTLPPSSNPTGAEFDPEEDEPTLEAAWPHLQLVYEFFLRFLESPDFQPNIAKKYIDQKFVLALLDLFDSEDPRERDFLKTILHRIYGKFLGLRAYIRRQINHIFYRFIYETEHHNGIAELLEILGSIINGFALPLKEEHKMFLIRVLLPLHKVKSLSVYHPQLAYCVVQFLEKESSLTEPVIVGLLKFWPKTHSPKEVMFLNELEEILDVIEPSEFSKVMEPLFRQLAKCVSSPHFQVAERALYYWNNEYIMSLISDNAARVLPIMFPALYRNSKSHWNKTIHGLIYNALKLFMEMNQKLFDDCTQQYKAEKQKGRFRMKEREEMWQKIEELARLNPQYPMFRAPPPLPPVYSMETETPTAEDIQLLKRTVETEAVQMLKDIKKEKVLLRRKSELPQDVYTIKALEAHKRAEEFLTASQEAL" 0.3) . }

Output format

----- json text xml csv

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