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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, and is hosted/served as a TRAPI API using Plover2.0. For more information about the RTX-KG2 knowledge graph and how we build it, see the RTX-KG2pre build system GitHub project area. For more information about the canonicalized version of RTX-KG2 (RTX-KG2c, which underlies the RTX-KG2 API), see the RTX-KG2c build system project area. For more information about the Plover2.0 platform, 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://kg2cploverdb.transltr.io/query" \
     -H  "accept: application/json" \
     -H  "Content-Type: application/json" \
     -d @onehop.json
should result in this response: 
{
  "logs":[
    {
      "level":"INFO",
      "message":"kg2c: Converting qnode n00's 'ids' to equivalent ids we recognize",
      "timestamp":"Fri, 15 Nov 2024 21:11:02 GMT"
    },
    ...
  "message": {
    "knowledge_graph": {
      "edges": {
        "30759528": {
          "attributes":[
            {
              "attribute_source":"infores:rtx-kg2",
              "attribute_type_id":"biolink:knowledge_level",
              "value":"knowledge_assertion"
            },
            {
              "attribute_source":"infores:rtx-kg2",
              "attribute_type_id":"biolink:original_predicate",
              "description":"The IDs of the original RTX-KG2pre edge(s) corresponding to this edge prior to any synonymization or remapping.",
              "value":[
                "CHEMBL.COMPOUND:CHEMBL112---biolink:physically_interacts_with---None---None---None---CHEMBL.TARGET:CHEMBL2094253---identifiers_org_registry:chembl.compound"
              ],
              "value_type_id":"metatype:String"
            },
            {
              "attribute_source":"infores:rtx-kg2",
              "attribute_type_id":"biolink:agent_type",
              "value":"manual_agent"
            }
          ],
          "object":"CHEMBL.TARGET:CHEMBL4523964",
          "predicate":"biolink:physically_interacts_with",
          "sources":[
            {
              "resource_id":"infores:chembl",
              "resource_role":"primary_knowledge_source"
            },
            {
              "resource_id":"infores:rtx-kg2",
              "resource_role":"aggregator_knowledge_source",
              "upstream_resource_ids":[
                "infores:chembl"
              ]
            }
          ],
          "subject":"CHEBI:46195"
        },
        ...

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/a6b575139cfd429b0a87f825a625d036 * Code for the build system for RTX-KG2pre: https://github.com/RTXteam/RTX-KG2 * Code for the build system for RTX-KG2c (canonicalized): https://github.com/RTXteam/RTX/tree/master/code/kg2c * Code for the Plover2.0 platform used to serve RTX-KG2: https://github.com/RTXteam/PloverDB