updated docs info

RobokopU24 · Oct 18, 2023 · b800af9 · b800af9
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diff --git a/api/openapi.json b/api/openapi.json
diff --git a/docs/automat/alliance-of-genome-resources-orthology.tag.mdx b/docs/automat/alliance-of-genome-resources-orthology.tag.mdx
diff --git a/docs/automat/alliance-of-genome-resources.tag.mdx b/docs/automat/alliance-of-genome-resources.tag.mdx
@@ -0,0 +1,33 @@
+---
+id: alliance-of-genome-resources
+title: "Alliance of Genome Resources"
+description: "Alliance of Genome Resources"
+custom_edit_url: null
+---
+
+
+
+
+The Alliance of Genome Resources is a consortium of the owners of seven model organism databases (MODs) and the Gene Ontology (GO) Consortium, whose goal is to provide an integrated view of their data to all biologists, clinicians, and other interested parties. The Alliance provides the results of all methods that have been benchmarked by the Quest for Orthologs Consortium (QfO), as well as curated ortholog inferences from HGNC (human, mouse, rat genes).
+
+**Version:** f713443719161796
+
+**URL:** [https://www.alliancegenome.org/](https://www.alliancegenome.org/)
+
+**Files:** [https://stars.renci.org/var/plater/bl-3.5.4/GenomeAllianceOrthologs_Automat/f713443719161796](https://stars.renci.org/var/plater/bl-3.5.4/GenomeAllianceOrthologs_Automat/f713443719161796)
+
+**Nodes:** 94,350
+
+**Edges:** 530,499
+
+
+
+
+
+```mdx-code-block
+import DocCardList from '@theme/DocCardList';
+import {useCurrentSidebarCategory} from '@docusaurus/theme-common';
+
+<DocCardList items={useCurrentSidebarCategory().items}/>
+```
+
diff --git a/docs/automat/binding.tag.mdx b/docs/automat/binding.tag.mdx
@@ -0,0 +1,33 @@
+---
+id: binding
+title: "BINDING"
+description: "BINDING"
+custom_edit_url: null
+---
+
+
+
+
+Binding DataBase (BindingDB) openly exposes curated data on chemical entities and their molecular targets.
+
+**Version:** 6ff4faf347a97f7f
+
+**URL:** [https://www.bindingdb.org/](https://www.bindingdb.org/)
+
+**Files:** [https://stars.renci.org/var/plater/bl-3.5.4/BINDING_Automat/6ff4faf347a97f7f](https://stars.renci.org/var/plater/bl-3.5.4/BINDING_Automat/6ff4faf347a97f7f)
+
+**Nodes:** 998,906
+
+**Edges:** 2,016,461
+
+
+
+
+
+```mdx-code-block
+import DocCardList from '@theme/DocCardList';
+import {useCurrentSidebarCategory} from '@docusaurus/theme-common';
+
+<DocCardList items={useCurrentSidebarCategory().items}/>
+```
+
diff --git a/docs/automat/cam-kp.tag.mdx b/docs/automat/cam-kp.tag.mdx
diff --git a/docs/automat/cam-provider-kg.tag.mdx b/docs/automat/cam-provider-kg.tag.mdx
@@ -0,0 +1,33 @@
+---
+id: cam-provider-kg
+title: "CAM Provider KG"
+description: "CAM Provider KG"
+custom_edit_url: null
+---
+
+
+
+
+The CAMP Provider KG contains data on CAMs (Causal Activity Models), which are small knowledge graphs built using the Web Ontology Language (OWL). The CAM database combines many CAM graphs, along with a large merged bio-ontology containing the full vocabulary of concepts referenced within the individual CAMs. Each CAM describes an instantiation of some of those concepts in a particular context, modeling the interactions between those instances as an interlinked representation of a complex biological or environmental process.
+
+**Version:** ded8cfcdee598475
+
+
+
+**Files:** [https://stars.renci.org/var/plater/bl-3.5.4/CAMKP_Automat/ded8cfcdee598475](https://stars.renci.org/var/plater/bl-3.5.4/CAMKP_Automat/ded8cfcdee598475)
+
+**Nodes:** 111,273
+
+**Edges:** 3,525,826
+
+
+
+
+
+```mdx-code-block
+import DocCardList from '@theme/DocCardList';
+import {useCurrentSidebarCategory} from '@docusaurus/theme-common';
+
+<DocCardList items={useCurrentSidebarCategory().items}/>
+```
+
diff --git a/docs/automat/ctd.tag.mdx b/docs/automat/ctd.tag.mdx
@@ -10,15 +10,15 @@ custom_edit_url: null
 
 The Comparative Toxicogenomics Database (CTD) is an open-source database that provides manually curated information about chemical-gene/protein, chemical-disease, and gene/protein-disease relationships, with additional support for the curated relationships provided by function and pathway data.
 
-**Version:** eb067a5f55c8a4dd
+**Version:** 20d3dfad16037510
 
 **URL:** [http://ctdbase.org/about/](http://ctdbase.org/about/)
 
-**Neo4J:** [https://stars.renci.org/var/plater/bl-3.2.1/CTD_Automat/eb067a5f55c8a4dd/graph_eb067a5f55c8a4dd.db.dump](https://stars.renci.org/var/plater/bl-3.2.1/CTD_Automat/eb067a5f55c8a4dd/graph_eb067a5f55c8a4dd.db.dump)
+**Files:** [https://stars.renci.org/var/plater/bl-3.5.4/CTD_Automat/20d3dfad16037510](https://stars.renci.org/var/plater/bl-3.5.4/CTD_Automat/20d3dfad16037510)
 
-**Nodes:** 441,863
+**Nodes:** 444,472
 
-**Edges:** 1,462,012
+**Edges:** 1,464,525
 
 
 

diff --git a/docs/automat/cypher-cypher-post-binding-db.api.mdx b/docs/automat/cypher-cypher-post-binding-db.api.mdx
@@ -0,0 +1,38 @@
+---
+id: cypher-cypher-post-binding-db
+title: "Run cypher query"
+description: "Runs cypher query against the Neo4j instance, and returns an equivalent response expected from a Neo4j HTTP endpoint (https://neo4j.com/docs/rest-docs/current/)."
+sidebar_label: "Run cypher query"
+hide_title: true
+hide_table_of_contents: true
+api: {"description":"Runs cypher query against the Neo4j instance, and returns an equivalent response expected from a Neo4j HTTP endpoint (https://neo4j.com/docs/rest-docs/current/).","operationId":"cypher_cypher_post_binding-db","requestBody":{"content":{"application/json":{"schema":{"title":"CypherRequest","required":["query"],"type":"object","properties":{"query":{"title":"Query","type":"string"}}},"example":{"query":"MATCH (n) RETURN count(n)"}}},"required":true},"responses":{"200":{"description":"Successful Response","content":{"application/json":{"schema":{"title":"CypherResponse","required":["results","errors"],"type":"object","properties":{"results":{"title":"Results","type":"array","items":{"title":"CypherResult","required":["columns","data"],"type":"object","properties":{"columns":{"title":"Columns","type":"array","items":{"type":"string"}},"data":{"title":"Data","type":"array","items":{"title":"CypherDatum","required":["row","meta"],"type":"object","properties":{"row":{"title":"Row","type":"array","items":{}},"meta":{"title":"Meta","type":"array","items":{}}}}}}}},"errors":{"title":"Errors","type":"array","items":{"title":"CypherError","required":["code","message"],"type":"object","properties":{"code":{"title":"Code","type":"string"},"message":{"title":"Message","type":"string"}}}}}}}}},"422":{"description":"Validation Error","content":{"application/json":{"schema":{"title":"HTTPValidationError","type":"object","properties":{"detail":{"title":"Detail","type":"array","items":{"title":"ValidationError","required":["loc","msg","type"],"type":"object","properties":{"loc":{"title":"Location","type":"array","items":{"anyOf":[{"type":"string"},{"type":"integer"}]}},"msg":{"title":"Message","type":"string"},"type":{"title":"Error Type","type":"string"}}}}}}}}}},"tags":["BINDING"],"method":"post","path":"/binding-db/cypher","servers":[{"url":"https://robokop-automat.apps.renci.org"}],"jsonRequestBodyExample":{"query":"string"},"info":{"title":"Automat","version":"2.1","termsOfService":"http://loading"},"postman":{"name":"Run cypher query","description":{"content":"Runs cypher query against the Neo4j instance, and returns an equivalent response expected from a Neo4j HTTP endpoint (https://neo4j.com/docs/rest-docs/current/).","type":"text/plain"},"url":{"path":["binding-db","cypher"],"host":["{{baseUrl}}"],"query":[],"variable":[]},"header":[{"key":"Content-Type","value":"application/json"},{"key":"Accept","value":"application/json"}],"method":"POST","body":{"mode":"raw","raw":"\"\"","options":{"raw":{"language":"json"}}}}}
+sidebar_class_name: "post api-method"
+info_path: docs/automat/automat
+custom_edit_url: null
+---
+
+import ApiTabs from "@theme/ApiTabs";
+import MimeTabs from "@theme/MimeTabs";
+import ParamsItem from "@theme/ParamsItem";
+import ResponseSamples from "@theme/ResponseSamples";
+import SchemaItem from "@theme/SchemaItem";
+import SchemaTabs from "@theme/SchemaTabs";
+import DiscriminatorTabs from "@theme/DiscriminatorTabs";
+import TabItem from "@theme/TabItem";
+
+## Run cypher query
+
+
+
+Runs cypher query against the Neo4j instance, and returns an equivalent response expected from a Neo4j HTTP endpoint (https://neo4j.com/docs/rest-docs/current/).
+
+<MimeTabs><TabItem label={"application/json"} value={"application/json-schema"}><details style={{}} data-collapsed={false} open={true}><summary style={{"textAlign":"left"}}><strong>Request Body</strong><strong style={{"fontSize":"var(--ifm-code-font-size)","color":"var(--openapi-required)"}}> required</strong></summary><div style={{"textAlign":"left","marginLeft":"1rem"}}></div><ul style={{"marginLeft":"1rem"}}><SchemaItem collapsible={false} name={"query"} required={true} schemaName={"Query"} qualifierMessage={undefined} schema={{"title":"Query","type":"string"}}></SchemaItem></ul></details></TabItem></MimeTabs><div><ApiTabs><TabItem label={"200"} value={"200"}><div>
+
+Successful Response
+
+</div><div><MimeTabs schemaType={"response"}><TabItem label={"application/json"} value={"application/json"}><SchemaTabs><TabItem label={"Schema"} value={"Schema"}><details style={{}} data-collapsed={false} open={true}><summary style={{"textAlign":"left"}}><strong>Schema</strong></summary><div style={{"textAlign":"left","marginLeft":"1rem"}}></div><ul style={{"marginLeft":"1rem"}}><SchemaItem collapsible={true} className={"schemaItem"}><details style={{}}><summary style={{}}><strong>results</strong><span style={{"opacity":"0.6"}}> object[]</span><strong style={{"fontSize":"var(--ifm-code-font-size)","color":"var(--openapi-required)"}}> required</strong></summary><div style={{"marginLeft":"1rem"}}><li><div style={{"fontSize":"var(--ifm-code-font-size)","opacity":"0.6","marginLeft":"-.5rem","paddingBottom":".5rem"}}>Array [</div></li><SchemaItem collapsible={false} name={"columns"} required={false} schemaName={"string[]"} qualifierMessage={undefined} schema={{"title":"Columns","type":"array","items":{"type":"string"}}}></SchemaItem><SchemaItem collapsible={true} className={"schemaItem"}><details style={{}}><summary style={{}}><strong>data</strong><span style={{"opacity":"0.6"}}> object[]</span><strong style={{"fontSize":"var(--ifm-code-font-size)","color":"var(--openapi-required)"}}> required</strong></summary><div style={{"marginLeft":"1rem"}}><li><div style={{"fontSize":"var(--ifm-code-font-size)","opacity":"0.6","marginLeft":"-.5rem","paddingBottom":".5rem"}}>Array [</div></li><SchemaItem collapsible={false} name={"row"} required={false} schemaName={"undefined[]"} qualifierMessage={undefined} schema={{"title":"Row","type":"array","items":{}}}></SchemaItem><SchemaItem collapsible={false} name={"meta"} required={false} schemaName={"undefined[]"} qualifierMessage={undefined} schema={{"title":"Meta","type":"array","items":{}}}></SchemaItem><li><div style={{"fontSize":"var(--ifm-code-font-size)","opacity":"0.6","marginLeft":"-.5rem"}}>]</div></li></div></details></SchemaItem><li><div style={{"fontSize":"var(--ifm-code-font-size)","opacity":"0.6","marginLeft":"-.5rem"}}>]</div></li></div></details></SchemaItem><SchemaItem collapsible={true} className={"schemaItem"}><details style={{}}><summary style={{}}><strong>errors</strong><span style={{"opacity":"0.6"}}> object[]</span><strong style={{"fontSize":"var(--ifm-code-font-size)","color":"var(--openapi-required)"}}> required</strong></summary><div style={{"marginLeft":"1rem"}}><li><div style={{"fontSize":"var(--ifm-code-font-size)","opacity":"0.6","marginLeft":"-.5rem","paddingBottom":".5rem"}}>Array [</div></li><SchemaItem collapsible={false} name={"code"} required={false} schemaName={"Code"} qualifierMessage={undefined} schema={{"title":"Code","type":"string"}}></SchemaItem><SchemaItem collapsible={false} name={"message"} required={false} schemaName={"Message"} qualifierMessage={undefined} schema={{"title":"Message","type":"string"}}></SchemaItem><li><div style={{"fontSize":"var(--ifm-code-font-size)","opacity":"0.6","marginLeft":"-.5rem"}}>]</div></li></div></details></SchemaItem></ul></details></TabItem><TabItem label={"Example (from schema)"} value={"Example (from schema)"}><ResponseSamples responseExample={"{\n  \"results\": [\n    {\n      \"columns\": [\n        \"string\"\n      ],\n      \"data\": [\n        {\n          \"row\": [\n            null\n          ],\n          \"meta\": [\n            null\n          ]\n        }\n      ]\n    }\n  ],\n  \"errors\": [\n    {\n      \"code\": \"string\",\n      \"message\": \"string\"\n    }\n  ]\n}"} language={"json"}></ResponseSamples></TabItem></SchemaTabs></TabItem></MimeTabs></div></TabItem><TabItem label={"422"} value={"422"}><div>
+
+Validation Error
+
+</div><div><MimeTabs schemaType={"response"}><TabItem label={"application/json"} value={"application/json"}><SchemaTabs><TabItem label={"Schema"} value={"Schema"}><details style={{}} data-collapsed={false} open={true}><summary style={{"textAlign":"left"}}><strong>Schema</strong></summary><div style={{"textAlign":"left","marginLeft":"1rem"}}></div><ul style={{"marginLeft":"1rem"}}><SchemaItem collapsible={true} className={"schemaItem"}><details style={{}}><summary style={{}}><strong>detail</strong><span style={{"opacity":"0.6"}}> object[]</span></summary><div style={{"marginLeft":"1rem"}}><li><div style={{"fontSize":"var(--ifm-code-font-size)","opacity":"0.6","marginLeft":"-.5rem","paddingBottom":".5rem"}}>Array [</div></li><SchemaItem collapsible={true} className={"schemaItem"}><details style={{}}><summary style={{}}><strong>loc</strong><span style={{"opacity":"0.6"}}> object[]</span><strong style={{"fontSize":"var(--ifm-code-font-size)","color":"var(--openapi-required)"}}> required</strong></summary><div style={{"marginLeft":"1rem"}}><li><div style={{"fontSize":"var(--ifm-code-font-size)","opacity":"0.6","marginLeft":"-.5rem","paddingBottom":".5rem"}}>Array [</div></li><li><span className={"badge badge--info"}>anyOf</span><SchemaTabs><TabItem label={"MOD1"} value={"0-item-properties"}><li><div><strong>string</strong></div></li></TabItem><TabItem label={"MOD2"} value={"1-item-properties"}><li><div><strong>integer</strong></div></li></TabItem></SchemaTabs></li><li><div style={{"fontSize":"var(--ifm-code-font-size)","opacity":"0.6","marginLeft":"-.5rem"}}>]</div></li></div></details></SchemaItem><SchemaItem collapsible={false} name={"msg"} required={false} schemaName={"Message"} qualifierMessage={undefined} schema={{"title":"Message","type":"string"}}></SchemaItem><SchemaItem collapsible={false} name={"type"} required={false} schemaName={"Error Type"} qualifierMessage={undefined} schema={{"title":"Error Type","type":"string"}}></SchemaItem><li><div style={{"fontSize":"var(--ifm-code-font-size)","opacity":"0.6","marginLeft":"-.5rem"}}>]</div></li></div></details></SchemaItem></ul></details></TabItem><TabItem label={"Example (from schema)"} value={"Example (from schema)"}><ResponseSamples responseExample={"{\n  \"detail\": [\n    {\n      \"loc\": [\n        \"string\",\n        0\n      ],\n      \"msg\": \"string\",\n      \"type\": \"string\"\n    }\n  ]\n}"} language={"json"}></ResponseSamples></TabItem></SchemaTabs></TabItem></MimeTabs></div></TabItem></ApiTabs></div>
+