-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
252 changed files
with
10,314 additions
and
3,750 deletions.
There are no files selected for viewing
Large diffs are not rendered by default.
Oops, something went wrong.
33 changes: 0 additions & 33 deletions
33
docs/automat/alliance-of-genome-resources-orthology.tag.mdx
This file was deleted.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -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}/> | ||
``` | ||
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -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}/> | ||
``` | ||
|
This file was deleted.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -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}/> | ||
``` | ||
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -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> | ||
|
Oops, something went wrong.