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RTX-KG2

RTX-KG2 Knowledge Provider Page

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RTX-KG2 is a Translator System Knowledge Provider created/supported/maintained by Team Expander Agent. It can answer Translator queries that are expressed in TRAPI format, with query graphs that contain one node or two nodes connected by an edge (i.e., a “one-hop” query). RTX-KG2 is backed by the RTX-KG2 knowledge graph, which integrates dozens of upstream knowledge sources into a Biolink-compliant system hosted in a custom in-memory database (PloverDB). For more information about the RTX-KG2 knowledge graph and how we built it, see the RTX-KG2 build system GitHub project area. For more information about the PloverDB database, see the PloverDB GitHub project area. RTX-KG2 is one of the KPs that is used by the Translator reasoning agent, ARAX. For more information about ARAX, see the Expander Agent Page.

Use Cases-

  • one-hop query:

cat <<EOF >onehop.json 
{
  "message":{
    "query_graph":{
      "nodes":{
        "n00":{
          "ids":["CHEMBL.COMPOUND:CHEMBL112"],
          "categories":[
            "biolink:Drug"
          ],
          "is_set":false
        },
        "n01":{
          "categories":[
            "biolink:Gene",
            "biolink:Protein"
          ],
          "is_set":false
        }
      },
      "edges":{
        "e00":{
          "predicates":[
            "biolink:interacts_with"
          ],
          "subject":"n00",
          "object":"n01",
          "exclude":false
        }
      }
    }
  }
}
EOF

curl -X POST \
     "https://kg2.transltr.io/api/rtxkg2/v1.4/query?bypass_cache=false" \
     -H  "accept: application/json" \
     -H  "Content-Type: application/json" \
     -d @onehop.json
should result in this response: 
{
  "context": "https://raw.githubusercontent.com/biolink/biolink-model/master/context.jsonld",
  "datetime": "2021-04-28 04:54:14",
  "description": "Normal completion",
  "logs": [
    {
      "code": "",
      "level": "INFO",
      "message": "RTXKG2 Query launching on incoming Query",
      "timestamp": "2021-04-28T04:54:14.856515"
    },
    ...
  ],
  "message": {
    "knowledge_graph": {
      "edges": {
        "1447028": {
          "attributes": [
            {
              "name": "provided_by",
              "type": "biolink:provided_by",
              "value": [
                "identifiers_org_registry:chembl.compound"
              ]
            }
          ],
          "object": "UniProtKB:O00519",
          "predicate": "biolink:molecularly_interacts_with",
          "subject": "CHEMBL.COMPOUND:CHEMBL112"
        },
        "1447029": {
          "attributes": [
            {
              "name": "provided_by",
              "type": "biolink:provided_by",
              "value": [
                "identifiers_org_registry:chembl.compound"
              ]
            }
          ],
          "object": "UniProtKB:O14965",
          "predicate": "biolink:molecularly_interacts_with",
          "subject": "CHEMBL.COMPOUND:CHEMBL112"
        },
        "1447030": {
          "attributes": [
            {
              "name": "provided_by",
              "type": "biolink:provided_by",
              "value": [
                "identifiers_org_registry:chembl.compound"
              ]
            }
          ],
          "object": "UniProtKB:O43570",
          "predicate": "biolink:molecularly_interacts_with",
          "subject": "CHEMBL.COMPOUND:CHEMBL112"
        },
        "1447031": {
          "attributes": [
            {
              "name": "provided_by",
              "type": "biolink:provided_by",
              "value": [
                "pharos:"
              ]
            }
          ],
          "object": "UniProtKB:P00797",
          "predicate": "biolink:molecularly_interacts_with",
          "subject": "CHEMBL.COMPOUND:CHEMBL112"
        },
        "1447032": {
          "attributes": [
            {
              "name": "provided_by",
              "type": "biolink:provided_by",
              "value": [
                "identifiers_org_registry:chembl.compound"
              ]
            }
          ],
          "object": "UniProtKB:P00915",
          "predicate": "biolink:molecularly_interacts_with",
          "subject": "CHEMBL.COMPOUND:CHEMBL112"
        },
        "1447033": {
          "attributes": [
            {
              "name": "provided_by",
              "type": "biolink:provided_by",
              "value": [
                "identifiers_org_registry:chembl.compound"
              ]
            }
          ],
          "object": "UniProtKB:P06746",
          "predicate": "biolink:molecularly_interacts_with",
          "subject": "CHEMBL.COMPOUND:CHEMBL112"
        },
        "1447034": {
          "attributes": [
            {
              "name": "provided_by",
              "type": "biolink:provided_by",
              "value": [
                "identifiers_org_registry:chembl.compound"
              ]
            }
          ],
          "object": "UniProtKB:P07550",
          "predicate": "biolink:molecularly_interacts_with",
          "subject": "CHEMBL.COMPOUND:CHEMBL112"
        },
        ...

Knowledge Sources Accessed - See the FAQ entry “What data sources are used in KG2?” for details. * Biolink model * ChEMBL * DGIdb * DisGeNET * DrugBank * DrugCentral * EFO * Ensembl (Ensembl Genes, for human) * Gene Ontology annotations (from EBI) * HMDB * IntAct * Jensen Lab Diseases * KEGG (via API) * miRBase * NCBI Gene * OBO Foundry ontologies * BFO * CHEBI * GO-plus * RO * UBERON * FMA * DDANAT * CL * FOODON * EHDAA2 * BSPO * HP * NBO * NCBI taxslim * PATO * MONDO * DOID * PR * INO * GENEPIO * MI * PathWhiz * Reactome * repoDB * SemMedDB * SMPDB * TTD * UMLS * UMLS Semantic Types * ATC * CPT * DRUGBANK * FMA * GO * HCPCS * HCPT * HGNC * HL7 * HPO * ICD10 * ICD10AE * ICD10CM * ICD10PCS * ICD9CM * LNC * MDR * MED-RT * MEDLINEPLUS * MESH * NCBI * NCI * NDDF * NDFRT * OMIM * PDQ * PSY * RXNORM * SNOMEDCT * VANDF * UniChem (cross-references between Chebi, ChEMBL compound, DrugBank, HMDB, KEGG, and DrugCentral identifiers) * UniProtKB

Source Code - (include links to your source code). See example below * Example python module that queries the KG2 KP API

External Documentation (List of urls for documentation sites). See example below. * SmartAPI registry page for RTX-KG2: https://smart-api.info/ui/00bab7d59abe031098d5cb1597f7f1c4 * Code for the build system for RTX-KG2: https://github.com/RTXteam/RTX/tree/master/code/kg2 * Code for PloverDB database used by RTX-KG2 service: https://github.com/RTXteam/PloverDB