Documentation updates from Team Expander Agent

.gitignore

@@ -132,3 +132,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# emacs backup files
+**/*~

docs/architecture/ara.md

@@ -13,8 +13,7 @@ Translator "Autonomous Relay Agents" (ARAs) build build upon the knowledge contr
 | Contact Team       | Name                                                               | Github Repository                                                           |
 |--------------------|--------------------------------------------------------------------|-----------------------------------------------------------------------------|
 | Ranking Agent      | Ranking Agent ('Aragorn')                                          | [ranking-agent/aragorn](https://github.com/ranking-agent/aragorn)           |
-| Expander Agent     | ARAX                                                               | [RTXteam/RTX](https://github.com/RTXteam/RTX)                               |
-| Expander Agent     | RTX-KG2                                                            | [RTXteam/RTX-KG2](https://github.com/RTXteam/RTX-KG2)                       |
+| [Expander Agent](../../teams/expander-agent)     | [ARAX](arax)                         | [RTXteam/RTX](https://github.com/RTXteam/RTX)                               |
 | Exposures Provider | ICEES                                                              | [NCATS-Tangerine/icees-api](https://github.com/NCATS-Tangerine/icees-api)   |
 | Exposures Provider | CAM-KP                                                             | [NCATS-Tangerine/cam-kp-api](https://github.com/NCATS-Tangerine/cam-kp-api) |
 | Genetics Provider  | Genetics Provider                                                  | [genetics-kp-dev](https://github.com/broadinstitute/genetics-kp-dev)        |

docs/architecture/kp.md

@@ -25,3 +25,4 @@ Knowledge Providers (KPs) contribute domain-specific, high-value information abs
 | Multiomics Provider     | Multiomics Wellness                | [Multiomics Wellness wiki page](https://github.com/NCATSTranslator/Translator-All/wiki/Wellness-KP)
 | Multiomics Provider     | EHR Clinical Risk                  | [EHR Clinical Risk wiki page](https://github.com/NCATSTranslator/Translator-All/wiki/EHR-Risk-KP)
 | Multiomics Provider     | Clinical Trials                    | [Clinical Trials github](https://github.com/Hadlock-Lab/Multiomics_ClinicalTrials_KP)
+| Expander Agent          | [RTX-KG2](rtx-kg2)                 | [RTXteam/RTX-KG2](https://github.com/RTXteam/RTX-KG2) |

docs/architecture/kp/rtx-kg2.md

@@ -0,0 +1,282 @@
+## RTX-KG2 Knowledge Provider Page
+[Back to Home](..)
+
+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).
+
+* _Modes of Access_ 
+
+    * 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)
+
+* Issues using the RTX-KG2 KP should be logged in the [RTX-KG2 issue tracker](https://github.com/RTXteam/RTX-KG2/issues).
+
+* _How to build your own instance for NCATS Deployment pipeline_
+
+
+**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://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"
+        },
+        ...   
+```
+
+**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)
+
+**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
+
+**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

docs/teams/expander-agent.md

@@ -0,0 +1,20 @@
+[**Back to Home**](../..)
+
+# Team Expander Agent
+
+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.
+
+## Team Contact:
+
+[email protected]
+
+## Expander Agent PIs:
+
+Steve Ramsey: [email protected]
+
+Eric Deutsch: [email protected]
+
+David Koslicki: [email protected]
+

mkdocs.yml

@@ -19,9 +19,11 @@ nav:
         - Autonomous Relay Agents:
           - Overview: architecture/ara.md
           - Biothings Explorer: "https://biothings.io/explorer/"
+          - ARAX: architecture/ara/arax.md
         - Knowledge Providers:
           - Overview: architecture/kp.md
           - Service Provider: architecture/kp/service_provider.md
+          - RTX-KG2: architecture/kp/rtx-kg2.md
         - Shared Standards and Tools:
           - Introduction: architecture/sri.md
           - Biolink Model: "https://biolink.github.io/biolink-model/"
@@ -40,5 +42,6 @@ nav:
             - Overview: guide-for-developers/testing.md
             - SRI Testing: guide-for-developers/sri_testing.md
         - The Full Monty...: guide-for-developers/details.md
-
+    - Teams:
+        - Expander Agent: teams/expander-agent.md
 theme: readthedocs