kegg_database

Name: kegg_database
Author: ai4protein

244stars35forks

How to install kegg_database?

ai4protein/venusfactory2/kegg_database

$npx -y skills add ai4protein/VenusFactory2 --skill kegg_database

Installs into the current project.

Summary

Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. Use this for direct HTTP/REST work or KEGG-specific control.

Files · 1

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SKILL.md

1	# KEGG Database
2
3	## Overview
4
5	KEGG (Kyoto Encyclopedia of Genes and Genomes) is a comprehensive bioinformatics resource for biological pathway analysis and molecular interaction networks. In this project the agent exposes only download tools: save database info, entry lists, search results, entry data, ID conversions, cross-references, and drug-drug interactions to files; each returns rich JSON `{status, file_info, content_preview, biological_metadata, execution_context}`. For programmatic use, the package also provides query-style APIs (see Project Modules).
6
7	Important: KEGG API is made available only for academic use by academic users.
8
9	## When to Use This Skill
10
11	This skill should be used when querying pathways, genes, compounds, enzymes, diseases, and drugs across multiple organisms using KEGG's REST API.
12
13	## Quick Start
14
15	The skill provides:
16	1. Project modules in `src/tools/database/kegg/`: `kegg_rest.py` (base HTTP client), `kegg_operations.py` (query/download operations), `kegg_api.py` (backward-compat re-exports); all download functions re-exported via package. For programmatic use, import e.g. `from src.tools.database.kegg import download_kegg_entry_by_id, ...`.
17	2. Reference: `references/kegg_reference.md`
18
19	### Agent Tools (Download Only)
20
21	\| Tool name \| Arguments \| Purpose \|
22	\|-----------\|-----------\|---------\|
23	\| `download_kegg_info_by_database` \| `database`, `out_path` \| Download KEGG database info/statistics to file \|
24	\| `download_kegg_list_by_database` \| `database`, `out_path`, `org_or_ids` (optional) \| Download KEGG entry list by database to file \|
25	\| `download_kegg_find_by_database` \| `database`, `query`, `out_path`, `option` (optional) \| Download KEGG search results to file \|
26	\| `download_kegg_entry_by_id` \| `entry_id`, `out_path`, `format` (optional) \| Download KEGG entry data by entry ID to file \|
27	\| `download_kegg_conv_by_id` \| `target_db`, `source_id`, `out_path` \| Download KEGG ID conversion result to file \|
28	\| `download_kegg_link_by_id` \| `target_db`, `source_id`, `out_path` \| Download KEGG cross-reference links to file \|
29	\| `download_kegg_ddi_by_id` \| `drug_id`, `out_path` \| Download KEGG drug-drug interaction data to file \|
30
31	All return rich JSON: `{status, file_info, content_preview, biological_metadata, execution_context}`. Academic use only.
32
33	### Project Modules (Programmatic Use)
34
35	\| Capability \| Function \| Module \| Purpose \|
36	\|------------\|----------\|--------\|---------\|
37	\| HTTP client \| `kegg_request(operation, *path_parts)` \| kegg_rest.py \| Base REST GET request, returns text \|
38	\| ID helper \| `_join_ids(entry_id)` \| kegg_rest.py \| Format one or multiple IDs for URL (max 10) \|
39	\| Query: info \| `query_kegg_info_by_database(database)` \| kegg_operations.py \| Returns rich JSON in memory \|
40	\| Query: list \| `query_kegg_list_by_database(database, org_or_ids)` \| kegg_operations.py \| Returns rich JSON in memory \|
41	\| Query: find \| `query_kegg_find_by_database(database, query, option)` \| kegg_operations.py \| Returns rich JSON in memory \|
42	\| Query: entry \| `query_kegg_entry_by_id(entry_id, format)` \| kegg_operations.py \| Returns rich JSON in memory \|
43	\| Query: conv \| `query_kegg_conv_by_id(target_db, source_id)` \| kegg_operations.py \| Returns rich JSON in memory \|
44	\| Query: link \| `query_kegg_link_by_id(target_db, source_id)` \| kegg_operations.py \| Returns rich JSON in memory \|
45	\| Query: ddi \| `query_kegg_ddi_by_id(drug_id)` \| kegg_operations.py \| Returns rich JSON in memory \|
46	\| Download: info \| `download_kegg_info_by_database(database, out_path)` \| kegg_operations.py \| Save to file, return rich JSON \|
47	\| Download: list \| `download_kegg_list_by_database(database, out_path, org_or_ids)` \| kegg_operations.py \| Save to file, return rich JSON \|
48	\| Download: find \| `download_kegg_find_by_database(database, query, out_path, option)` \| kegg_operations.py \| Save to file, return rich JSON \|
49	\| Download: entry \| `download_kegg_entry_by_id(entry_id, out_path, format)` \| kegg_operations.py \| Save to file, return rich JSON \|
50	\| Download: conv \| `download_kegg_conv_by_id(target_db, source_id, out_path)` \| kegg_operations.py \| Save to file, return rich JSON \|
51	\| Download: link \| `download_kegg_link_by_id(target_db, source_id, out_path)` \| kegg_operations.py \| Save to file, return rich JSON \|
52	\| Download: ddi \| `download_kegg_ddi_by_id(drug_id, out_path)` \| kegg_operations.py \| Save to file, return rich JSON \|
53	\| Compat alias \| `kegg_info`, `kegg_list`, `kegg_find`, `kegg_get`, `kegg_conv`, `kegg_link`, `kegg_ddi` \| kegg_operations.py \| Backward-compat aliases for query functions \|
54
55	## Core Capabilities
56
57	### 1. Database Information
58
59	Download database info:
60	```python
61	fro

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Type

kegg_database

244stars35forks

View on GitHub

How to install kegg_database?

ai4protein/venusfactory2/kegg_database

$npx -y skills add ai4protein/VenusFactory2 --skill kegg_database

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	# KEGG Database
2
3	## Overview
4
5	KEGG (Kyoto Encyclopedia of Genes and Genomes) is a comprehensive bioinformatics resource for biological pathway analysis and molecular interaction networks. In this project the agent exposes only download tools: save database info, entry lists, search results, entry data, ID conversions, cross-references, and drug-drug interactions to files; each returns rich JSON `{status, file_info, content_preview, biological_metadata, execution_context}`. For programmatic use, the package also provides query-style APIs (see Project Modules).
6
7	Important: KEGG API is made available only for academic use by academic users.
8
9	## When to Use This Skill
10
11	This skill should be used when querying pathways, genes, compounds, enzymes, diseases, and drugs across multiple organisms using KEGG's REST API.
12
13	## Quick Start
14
15	The skill provides:
16	1. Project modules in `src/tools/database/kegg/`: `kegg_rest.py` (base HTTP client), `kegg_operations.py` (query/download operations), `kegg_api.py` (backward-compat re-exports); all download functions re-exported via package. For programmatic use, import e.g. `from src.tools.database.kegg import download_kegg_entry_by_id, ...`.
17	2. Reference: `references/kegg_reference.md`
18
19	### Agent Tools (Download Only)
20
21	\| Tool name \| Arguments \| Purpose \|
22	\|-----------\|-----------\|---------\|
23	\| `download_kegg_info_by_database` \| `database`, `out_path` \| Download KEGG database info/statistics to file \|
24	\| `download_kegg_list_by_database` \| `database`, `out_path`, `org_or_ids` (optional) \| Download KEGG entry list by database to file \|
25	\| `download_kegg_find_by_database` \| `database`, `query`, `out_path`, `option` (optional) \| Download KEGG search results to file \|
26	\| `download_kegg_entry_by_id` \| `entry_id`, `out_path`, `format` (optional) \| Download KEGG entry data by entry ID to file \|
27	\| `download_kegg_conv_by_id` \| `target_db`, `source_id`, `out_path` \| Download KEGG ID conversion result to file \|
28	\| `download_kegg_link_by_id` \| `target_db`, `source_id`, `out_path` \| Download KEGG cross-reference links to file \|
29	\| `download_kegg_ddi_by_id` \| `drug_id`, `out_path` \| Download KEGG drug-drug interaction data to file \|
30
31	All return rich JSON: `{status, file_info, content_preview, biological_metadata, execution_context}`. Academic use only.
32
33	### Project Modules (Programmatic Use)
34
35	\| Capability \| Function \| Module \| Purpose \|
36	\|------------\|----------\|--------\|---------\|
37	\| HTTP client \| `kegg_request(operation, *path_parts)` \| kegg_rest.py \| Base REST GET request, returns text \|
38	\| ID helper \| `_join_ids(entry_id)` \| kegg_rest.py \| Format one or multiple IDs for URL (max 10) \|
39	\| Query: info \| `query_kegg_info_by_database(database)` \| kegg_operations.py \| Returns rich JSON in memory \|
40	\| Query: list \| `query_kegg_list_by_database(database, org_or_ids)` \| kegg_operations.py \| Returns rich JSON in memory \|
41	\| Query: find \| `query_kegg_find_by_database(database, query, option)` \| kegg_operations.py \| Returns rich JSON in memory \|
42	\| Query: entry \| `query_kegg_entry_by_id(entry_id, format)` \| kegg_operations.py \| Returns rich JSON in memory \|
43	\| Query: conv \| `query_kegg_conv_by_id(target_db, source_id)` \| kegg_operations.py \| Returns rich JSON in memory \|
44	\| Query: link \| `query_kegg_link_by_id(target_db, source_id)` \| kegg_operations.py \| Returns rich JSON in memory \|
45	\| Query: ddi \| `query_kegg_ddi_by_id(drug_id)` \| kegg_operations.py \| Returns rich JSON in memory \|
46	\| Download: info \| `download_kegg_info_by_database(database, out_path)` \| kegg_operations.py \| Save to file, return rich JSON \|
47	\| Download: list \| `download_kegg_list_by_database(database, out_path, org_or_ids)` \| kegg_operations.py \| Save to file, return rich JSON \|
48	\| Download: find \| `download_kegg_find_by_database(database, query, out_path, option)` \| kegg_operations.py \| Save to file, return rich JSON \|
49	\| Download: entry \| `download_kegg_entry_by_id(entry_id, out_path, format)` \| kegg_operations.py \| Save to file, return rich JSON \|
50	\| Download: conv \| `download_kegg_conv_by_id(target_db, source_id, out_path)` \| kegg_operations.py \| Save to file, return rich JSON \|
51	\| Download: link \| `download_kegg_link_by_id(target_db, source_id, out_path)` \| kegg_operations.py \| Save to file, return rich JSON \|
52	\| Download: ddi \| `download_kegg_ddi_by_id(drug_id, out_path)` \| kegg_operations.py \| Save to file, return rich JSON \|
53	\| Compat alias \| `kegg_info`, `kegg_list`, `kegg_find`, `kegg_get`, `kegg_conv`, `kegg_link`, `kegg_ddi` \| kegg_operations.py \| Backward-compat aliases for query functions \|
54
55	## Core Capabilities
56
57	### 1. Database Information
58
59	Download database info:
60	```python
61	fro

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Type