-
Notifications
You must be signed in to change notification settings - Fork 17
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
add service provider, exploring agent documentation (#59)
- Loading branch information
Showing
9 changed files
with
233 additions
and
34 deletions.
There are no files selected for viewing
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 +1,73 @@ | ||
| [Back to ARAs](index.md) | ||
|
|
||
| # BioThings Explorer Autonomous Relay Agent Page | ||
|
|
||
| BioThings Explorer (BTE) is an application supported by Exploring Agent. The service queries a virtual, federated knowledge graph derived from the aggregated information in a network of biomedical web services. BTE leverages semantically precise annotations of the inputs and outputs for each resource (captured in the [SmartAPI registry](https://smart-api.info/)) and automates the chaining of web service calls to execute multi-step graph queries. Because there is no large, centralized knowledge graph to maintain, BTE is distributed as a lightweight application that dynamically retrieves information at query time. More information about BioThings Explorer can be found at [https://explorer.biothings.io](https://explorer.biothings.io). | ||
|
|
||
| The scoring/ranking of results in BTE incorporates a number of factors, including: | ||
|
|
||
| - the number of paths connecting the query node to the answer node | ||
| - the length of each path | ||
| - the number of redundant paths/edges | ||
| - the provenance of the edges (e.g., text-mined versus curated) | ||
| - the [Normalized Google Distance](https://en.wikipedia.org/wiki/Normalized_Google_distance) between nodes in the path | ||
|
|
||
| BTE is registered on SmartAPI [here](https://smart-api.info/ui/dc91716f44207d2e1287c727f281d339). If you would like to deploy your own instance, see the [installation documentation](https://github.com/biothings/biothings_explorer/blob/main/docs/INSTALLATION.md). | ||
|
|
||
| ## Use Cases | ||
|
|
||
| ```sh | ||
| echo '{ | ||
| "message": { | ||
| "query_graph": { | ||
| "nodes": { | ||
| "n02": { | ||
| "categories": [ | ||
| "biolink:Disease" | ||
| ], | ||
| "ids": [ | ||
| "MONDO:0005148" | ||
| ] | ||
| }, | ||
| "n01": { | ||
| "categories": [ | ||
| "biolink:ChemicalEntity" | ||
| ] | ||
| } | ||
| }, | ||
| "edges": { | ||
| "e01": { | ||
| "subject": "n01", | ||
| "object": "n02", | ||
| "predicates": [ | ||
| "biolink:treats" | ||
| ], | ||
| "knowledge_type": "inferred" | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| ' > creative.json | ||
|
|
||
| # An inferred-mode query | ||
| curl -X POST \ | ||
| "https://bte.transltr.io/v1/query" \ | ||
| -H "Content-Type: application/json" \ | ||
| -H "accept: application/json" \ | ||
| -d @creative.json | ||
| ``` | ||
|
|
||
| ## Knowledge Providers Accessed | ||
|
|
||
| BioThings Explorer maintains a allow-list of Knowledge Providers, see [here](https://github.com/biothings/bte-server/blob/main/config/api_list.yaml). | ||
|
|
||
| ## Source Code | ||
|
|
||
| [https://github.com/biothings/biothings_explorer](https://github.com/biothings/biothings_explorer) - Primary code repository for BioThings Explorer | ||
|
|
||
| ## Additional Links | ||
|
|
||
| - [Exploring Agent](https://github.com/NCATSTranslator/Translator-All/wiki/Exploring-Agent/) | ||
| - Preprint: [BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs](https://arxiv.org/abs/2304.09344) | ||
| - [BioThings Explorer Home Page](https://explorer.biothings.io/) |
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
Oops, something went wrong.