Extract all parents of a given node

Question

I\'m trying to extract all parents of a each given GO Id (a node) using EBI-RDF sparql endpoint, I was based on this two similar questions to formulate the query, here\'re two e

Answer 1

Thanks to @AKSW I found a decent solution using HyperGraphQL (a GraphQL interface for querying and serving linked data on the Web).

I'll leave the detailed answer here, it may help someone.

1. I downloaded and set up HyperGraphQL download page

2. Linked it to EBI Sparql endpoint as described in this tutorial

   The config.json file I used:

   {
       "name": "ebi-hgql",
       "schema": "ebischema.graphql",
       "server": {
           "port": 8081,
           "graphql": "/graphql",
           "graphiql": "/graphiql"
       },
       "services": [
           {
               "id": "ebi-sparql",
               "type": "SPARQLEndpointService",
               "url": "http://www.ebi.ac.uk/rdf/services/sparql",
               "graph": "http://rdf.ebi.ac.uk/dataset/go",
               "user": "",
               "password": ""
           }
       ]
   }
   

   Here's how my ebischema.graphql file looks like (Since I needed only the Class, id, label and subClassOf):

   type __Context {
       Class:          _@href(iri: "http://www.w3.org/2002/07/owl#Class")
       id:             _@href(iri: "http://www.geneontology.org/formats/oboInOwl#id")
       label:          _@href(iri: "http://www.w3.org/2000/01/rdf-schema#label")
       subClassOf:     _@href(iri: "http://www.w3.org/2000/01/rdf-schema#subClassOf")
   }
   
   type Class @service(id:"ebi-sparql") {
       id: [String] @service(id:"ebi-sparql")
       label: [String] @service(id:"ebi-sparql")
       subClassOf: [Class] @service(id:"ebi-sparql")
   }
   

3. I started testing some simple query, but constantly getting an empty response; the answer to this issue solved my problem.

4. Finally I constructed the query to get the tree

   Using this query:

   {
     Class_GET_BY_ID(uris:[
       "http://purl.obolibrary.org/obo/GO_0032259",
       "http://purl.obolibrary.org/obo/GO_0007267"]) {
       id
       label
       subClassOf {
         id
         label
         subClassOf {
           id
           label
         }
       }
     }
   }
   

   I got some interesting results:

   {
     "extensions": {},
     "data": {
       "@context": {
         "_type": "@type",
         "_id": "@id",
         "id": "http://www.geneontology.org/formats/oboInOwl#id",
         "label": "http://www.w3.org/2000/01/rdf-schema#label",
         "Class_GET_BY_ID": "http://hypergraphql.org/query/Class_GET_BY_ID",
         "subClassOf": "http://www.w3.org/2000/01/rdf-schema#subClassOf"
       },
       "Class_GET_BY_ID": [
         {
           "id": [
             "GO:0032259"
           ],
           "label": [
             "methylation"
           ],
           "subClassOf": [
             {
               "id": [
                 "GO:0008152"
               ],
               "label": [
                 "metabolic process"
               ],
               "subClassOf": [
                 {
                   "id": [
                     "GO:0008150"
                   ],
                   "label": [
                     "biological_process"
                   ]
                 }
               ]
             }
           ]
         },
         {
           "id": [
             "GO:0007267"
           ],
           "label": [
             "cell-cell signaling"
           ],
           "subClassOf": [
             {
               "id": [
                 "GO:0007154"
               ],
               "label": [
                 "cell communication"
               ],
               "subClassOf": [
                 {
                   "id": [
                     "GO:0009987"
                   ],
                   "label": [
                     "cellular process"
                   ]
                 }
               ]
             },
             {
               "id": [
                 "GO:0023052"
               ],
               "label": [
                 "signaling"
               ],
               "subClassOf": [
                 {
                   "id": [
                     "GO:0008150"
                   ],
                   "label": [
                     "biological_process"
                   ]
                 }
               ]
             }
           ]
         }
       ]
     },
     "errors": []
   }
   

EDIT

This was exactly what I wanted, but I noticed that I can't add another sublevel like this:

{
  Class_GET_BY_ID(uris:[
    "http://purl.obolibrary.org/obo/GO_0032259",
    "http://purl.obolibrary.org/obo/GO_0007267"]) {
    id
    label
    subClassOf {
      id
      label
      subClassOf {
        id
        label
        subClassOf {  # <--- 4th sublevel
          id
          label
        }
      }
    }
  }
}

I created a new question: Endpoint returned Content-Type: text/html which is not recognized for SELECT queries