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Documentation updates from Team Expander Agent (#38)
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| # Pyre type checker | ||
| .pyre/ | ||
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| # emacs backup files | ||
| **/*~ | ||
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| ## RTX-KG2 Knowledge Provider Page | ||
| [Back to Home](..) | ||
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| RTX-KG2 is a Translator System Knowledge Provider created/supported/maintained | ||
| by | ||
| [Team Expander Agent](../../../teams/expander-agent). It | ||
| can answer Translator queries that are expressed in | ||
| [TRAPI](https://github.com/NCATSTranslator/ReasonerAPI) 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](https://github.com/RTXteam/RTX-KG2). For | ||
| more information about the PloverDB database, see the | ||
| [PloverDB GitHub project area](https://github.com/RTXteam/PloverDB). 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](../../../teams/expander-agent). | ||
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| * _Modes of Access_ | ||
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| * Via the Translator API (TRAPI) interface; see [the SmartAPI registry](https://smart-api.info/ui/00bab7d59abe031098d5cb1597f7f1c4) | ||
| * Download RTX-KG2 knowledge graph in [KGX TSV](https://github.com/biolink/kgx/blob/master/specification/kgx-format.md) format from the [NCATS GitHub git-lfs repository](https://github.com/ncats/translator-lfs-artifacts/tree/main/files). | ||
| * Build your own RTX-KG2: [instructions here](https://github.com/RTXteam/RTX-KG2#how-to-build-rtx-kg2-from-its-upstream-sources) | ||
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| * Issues using the RTX-KG2 KP should be logged in the [RTX-KG2 issue tracker](https://github.com/RTXteam/RTX-KG2/issues). | ||
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| * _How to build your own instance for NCATS Deployment pipeline_ | ||
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| **Use Cases**- | ||
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| * one-hop query: | ||
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| ``` | ||
| 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://arax.ncats.io/api/rtxkg2/v1.3/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" | ||
| }, | ||
| ... | ||
| ``` | ||
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| **Knowledge Sources Accessed** - See the [FAQ entry "What data sources are used in KG2?"](https://github.com/RTXteam/RTX/tree/master/code/kg2#what-data-sources-are-used-in-kg2) for details. | ||
| * [Biolink model](https://biolink.github.io/biolink-model/) | ||
| * [ChEMBL](https://www.ebi.ac.uk/chembl/) | ||
| * [DGIdb](https://www.dgidb.org/) | ||
| * [DisGeNET](https://www.disgenet.org/) | ||
| * [DrugBank](https://go.drugbank.com) | ||
| * [DrugCentral](https://drugcentral.org/) | ||
| * [EFO](https://www.ebi.ac.uk/efo/) | ||
| * [Ensembl](https://ensembl.org) (Ensembl Genes, for human) | ||
| * [Gene Ontology annotations](https://www.ebi.ac.uk/GOA/index) (from EBI) | ||
| * [HMDB](https://hmdb.ca) | ||
| * [IntAct](https://www.ebi.ac.uk/intact/) | ||
| * [Jensen Lab Diseases](https://diseases.jensenlab.org/) | ||
| * [KEGG](https://www.genome.jp/kegg/) (via API) | ||
| * [miRBase](https://mirbase.org) | ||
| * [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene) | ||
| * [OBO Foundry ontologies](http://www.obofoundry.org/) | ||
| * BFO | ||
| * CHEBI | ||
| * GO-plus | ||
| * RO | ||
| * UBERON | ||
| * FMA | ||
| * DDANAT | ||
| * CL | ||
| * FOODON | ||
| * EHDAA2 | ||
| * BSPO | ||
| * HP | ||
| * NBO | ||
| * NCBI taxslim | ||
| * PATO | ||
| * MONDO | ||
| * DOID | ||
| * PR | ||
| * INO | ||
| * GENEPIO | ||
| * MI | ||
| * [PathWhiz](https://smpdb.ca/pathwhiz) | ||
| * [Reactome](https://reactome.org) | ||
| * [repoDB](https://portal.dbmi.hms.harvard.edu/projects/repoDB/) | ||
| * [SemMedDB](https://skr3.nlm.nih.gov/SemMedDB/) | ||
| * [SMPDB](https://smpdb.ca) | ||
| * [TTD](http://db.idrblab.net/ttd/) | ||
| * [UMLS](https://www.nlm.nih.gov/research/umls/index.html) | ||
| * 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](https://www.ebi.ac.uk/unichem/) (cross-references between Chebi, ChEMBL compound, DrugBank, HMDB, KEGG, and DrugCentral identifiers) | ||
| * [UniProtKB](https://www.uniprot.org/help/uniprotkb) | ||
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| **Source Code** - (include links to your source code). See example below | ||
| * Example [python module](https://github.com/RTXteam/RTX/blob/master/code/ARAX/Examples/kg2_api_example.py) that queries the KG2 KP API | ||
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| **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 |
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| [**Back to Home**](../..) | ||
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| # Team Expander Agent | ||
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| Expander Agent is the team responsible for the | ||
| ["ARAX"](../../architecture/ara/arax) autonomous relay agent and the | ||
| ["RTX-KG2"](../../architecture/kp/rtx-kg2) knowledge provider. | ||
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| ## Team Contact: | ||
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| [email protected] | ||
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| ## Expander Agent PIs: | ||
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| Steve Ramsey: [email protected] | ||
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| Eric Deutsch: [email protected] | ||
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| David Koslicki: [email protected] | ||
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