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.

Two additional functions select the prediction model and expose its internals (the original dg:deepgo function is unchanged):

• dg:predict(?sequence ?threshold ?predictor) — like dg:deepgo but takes an extra predictor argument, e.g. "dgpp-light" (the DeepGO-PlusPlus-Light ensemble) or "deepgoplus" (default).
• dg:components(?sequence ?threshold ?predictor) — returns each individual predictor substream (DIAMOND, STRING-Net, hierarchy-aware CNN, ESM2-kNN, ProteInfer) separately; the first variable binds the component name.

Example queries:

• Example 1: Simple DG++Light query
• Example 2: Federated query which runs deepgo on two sequences from UniProt SPARQL Endpoint
• Example 3: Run the DeepGO-PlusPlus-Light model via dg:predict
• Example 4: Inspect the individual predictor substreams via dg:components

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:predict("MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGAEKAVQVKVKALPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLSPLHSVYVDQWDWERVMGDGERQFSTLKSTVEAIWAGIKATEAAVSEEFGLAPFLPDQIHFVHSQELLSRYPDLDAKGRERAIAKDLGAVFLVGIGGKLSDGHRHDVRAPDYDDWSTPSELGHAGLNGDILVWNPVLEDAFELSSMGIRVDADTLKHQLALTGDEDRLELEWHQALLRGEMPQTIGGGIGQSRLTMLLLQLPHIGQVQAGVWPAAVRESVPSLL" 0.5 "dgpp-light") . } LIMIT 20 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) . } 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:predict("MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGAEKAVQVKVKALPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLSPLHSVYVDQWDWERVMGDGERQFSTLKSTVEAIWAGIKATEAAVSEEFGLAPFLPDQIHFVHSQELLSRYPDLDAKGRERAIAKDLGAVFLVGIGGKLSDGHRHDVRAPDYDDWSTPSELGHAGLNGDILVWNPVLEDAFELSSMGIRVDADTLKHQLALTGDEDRLELEWHQALLRGEMPQTIGGGIGQSRLTMLLLQLPHIGQVQAGVWPAAVRESVPSLL" 0.5 "dgpp-light") . } LIMIT 20 PREFIX dg: <http://deepgoplus.bio2vec.net/functions#> PREFIX GO: <http://purl.obolibrary.org/obo/GO_> SELECT ?component ?go ?label ?score { (?component ?go ?label ?score) dg:components("MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGAEKAVQVKVKALPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLSPLHSVYVDQWDWERVMGDGERQFSTLKSTVEAIWAGIKATEAAVSEEFGLAPFLPDQIHFVHSQELLSRYPDLDAKGRERAIAKDLGAVFLVGIGGKLSDGHRHDVRAPDYDDWSTPSELGHAGLNGDILVWNPVLEDAFELSSMGIRVDADTLKHQLALTGDEDRLELEWHQALLRGEMPQTIGGGIGQSRLTMLLLQLPHIGQVQAGVWPAAVRESVPSLL" 0.5 "dgpp-light") . } LIMIT 20

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:predict("MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGAEKAVQVKVKALPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLSPLHSVYVDQWDWERVMGDGERQFSTLKSTVEAIWAGIKATEAAVSEEFGLAPFLPDQIHFVHSQELLSRYPDLDAKGRERAIAKDLGAVFLVGIGGKLSDGHRHDVRAPDYDDWSTPSELGHAGLNGDILVWNPVLEDAFELSSMGIRVDADTLKHQLALTGDEDRLELEWHQALLRGEMPQTIGGGIGQSRLTMLLLQLPHIGQVQAGVWPAAVRESVPSLL" 0.5 "dgpp-light") . } LIMIT 20

Output format

text json xml csv

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