@wentorai/research-plugins 1.3.1 → 1.4.0

package/skills/literature/search/paper-search-mcp-guide/SKILL.md

@@ -1,107 +0,0 @@
----
-name: paper-search-mcp-guide
-description: "MCP server for searching papers across arXiv, PubMed, bioRxiv"
-metadata:
-  openclaw:
-    emoji: "🔍"
-    category: "literature"
-    subcategory: "search"
-    keywords: ["paper search", "MCP", "arXiv", "PubMed", "bioRxiv", "multi-database"]
-    source: "wentor-research-plugins"
----
-
-# Paper Search MCP Guide
-
-## Overview
-
-Paper Search MCP is an MCP server that provides unified paper search across multiple academic databases — arXiv, PubMed, bioRxiv, and medRxiv. AI agents can search, download, and analyze papers through a single MCP interface. Handles API authentication, rate limiting, and result normalization across different database formats.
-
-## MCP Configuration
-
-```json
-{
-  "mcpServers": {
-    "paper-search": {
-      "command": "npx",
-      "args": ["@openags/paper-search-mcp"],
-      "env": {}
-    }
-  }
-}
-```
-
-## Available Tools
-
-```markdown
-### search_papers
-Search across all databases or specific ones.
-- query: Search terms
-- source: "arxiv" | "pubmed" | "biorxiv" | "all"
-- max_results: Number of results (default 10)
-- date_from: Start date filter
-- date_to: End date filter
-
-### get_paper
-Get full details for a specific paper.
-- id: arXiv ID, PMID, or DOI
-
-### download_pdf
-Download paper PDF.
-- id: Paper identifier
-- output_dir: Save location
-
-### get_references
-Get references cited by a paper.
-- id: Paper identifier
-
-### get_citations
-Get papers that cite this paper.
-- id: Paper identifier
-```
-
-## Usage in Agent Chat
-
-```markdown
-### Example Interactions
-
-"Search for recent papers on protein folding"
-→ Searches arXiv + PubMed + bioRxiv, returns unified results
-
-"Download the PDF for arxiv:2401.12345"
-→ Fetches and saves PDF locally
-
-"What papers cite the AlphaFold2 paper?"
-→ Looks up forward citations via Semantic Scholar
-
-"Find PubMed papers on CRISPR therapy from 2024"
-→ PubMed-specific search with date filter
-```
-
-## Normalized Result Format
-
-```json
-{
-  "title": "Paper Title",
-  "authors": ["Author A", "Author B"],
-  "abstract": "Abstract text...",
-  "source": "arxiv",
-  "id": "2401.12345",
-  "doi": "10.48550/arXiv.2401.12345",
-  "url": "https://arxiv.org/abs/2401.12345",
-  "published": "2024-01-15",
-  "categories": ["cs.AI", "cs.CL"]
-}
-```
-
-## Use Cases
-
-1. **Literature search**: Multi-database paper discovery
-2. **Agent research**: Automated paper retrieval for AI agents
-3. **PDF collection**: Bulk paper downloading
-4. **Citation analysis**: Forward and backward citation chains
-5. **Cross-database**: Unified search across arXiv + PubMed + bioRxiv
-
-## References
-
-- [paper-search-mcp GitHub](https://github.com/openags/paper-search-mcp)
-- [MCP Specification](https://modelcontextprotocol.io/)

package/skills/tools/knowledge-graph/paperpile-notion-guide/SKILL.md

@@ -1,84 +0,0 @@
----
-name: paperpile-notion-guide
-description: "Sync Paperpile references and annotations to Notion"
-metadata:
-  openclaw:
-    emoji: "📋"
-    category: "tools"
-    subcategory: "knowledge-graph"
-    keywords: ["Paperpile", "Notion", "sync", "reference management", "annotations", "integration"]
-    source: "https://github.com/gsarti/paperpile-notion"
----
-
-# Paperpile-Notion Integration Guide
-
-## Overview
-
-Paperpile-Notion is a tool that syncs your Paperpile reference library to a Notion database. It exports paper metadata (title, authors, year, DOI, abstract), reading status, labels, and annotations to Notion pages, enabling you to combine reference management with Notion's rich knowledge management features.
-
-## Setup
-
-```bash
-# Install from source
-git clone https://github.com/gsarti/paperpile-notion.git
-cd paperpile-notion
-pip install -e .
-
-# Configuration
-# 1. Export Paperpile library as BibTeX/JSON
-# 2. Create Notion integration and get token
-# 3. Create Notion database with required properties
-# 4. Run sync script
-```
-
-## Notion Database Properties
-
-```markdown
-### Required Properties
-| Property | Type | Source |
-|----------|------|--------|
-| Title | Title | Paper title |
-| Authors | Rich text | Author names |
-| Year | Number | Publication year |
-| DOI | URL | Digital Object Identifier |
-| Abstract | Rich text | Paper abstract |
-| Labels | Multi-select | Paperpile labels/folders |
-| Status | Select | Read / Unread / Reading |
-| Added | Date | Date added to Paperpile |
-| Journal | Rich text | Publication venue |
-| Notes | Rich text | Paperpile notes |
-```
-
-## Sync Workflow
-
-```python
-from paperpile_notion import PaperpileSync
-
-sync = PaperpileSync(
-    paperpile_export="library.bib",    # BibTeX export
-    notion_database_id="your_db_id",
-)
-
-# Full sync
-result = sync.run()
-print(f"Synced: {result.created} new, "
-      f"{result.updated} updated, "
-      f"{result.skipped} unchanged")
-
-# Incremental sync (only new/modified)
-result = sync.run(incremental=True)
-```
-
-## Use Cases
-
-1. **Knowledge management**: Paperpile references in Notion
-2. **Reading tracking**: Kanban board for paper reading status
-3. **Team collaboration**: Shared reference database in Notion
-4. **Research notes**: Rich notes alongside paper metadata
-5. **Project organization**: Tag papers by research project
-
-## References
-
-- [paperpile-notion GitHub](https://github.com/gsarti/paperpile-notion)
-- [Paperpile](https://paperpile.com/)
-- [Notion API](https://developers.notion.com/)

package/src/tools/semantic-scholar.ts

@@ -1,112 +0,0 @@
-import { Type } from "@sinclair/typebox";
-import type { OpenClawPluginApi, OpenClawPluginToolContext } from "openclaw/plugin-sdk";
-import { toolResult } from "./util.js";
-
-const BASE = "https://api.semanticscholar.org/graph/v1";
-
-export function createSemanticScholarTools(
-  ctx: OpenClawPluginToolContext,
-  api: OpenClawPluginApi,
-) {
-  const apiKey =
-    ctx.config?.get?.("plugins.entries.research-plugins.semanticScholarApiKey") ?? "";
-
-  const headers: Record<string, string> = apiKey ? { "x-api-key": apiKey } : {};
-
-  return [
-    {
-      name: "search_papers",
-      label: "Search Papers (Semantic Scholar)",
-      description:
-        "Search academic papers on Semantic Scholar. Returns titles, abstracts, authors, citation counts.",
-      parameters: Type.Object({
-        query: Type.String({ description: "Search query keywords" }),
-        limit: Type.Optional(
-          Type.Number({ description: "Max results to return (default 10, max 100)" }),
-        ),
-        year: Type.Optional(
-          Type.String({ description: "Year filter, e.g. '2024' or '2020-2024'" }),
-        ),
-        fields_of_study: Type.Optional(
-          Type.String({
-            description:
-              "Comma-separated fields, e.g. 'Computer Science,Mathematics'",
-          }),
-        ),
-        open_access_only: Type.Optional(
-          Type.Boolean({ description: "Only return open access papers" }),
-        ),
-      }),
-      execute: async (input: {
-        query: string;
-        limit?: number;
-        year?: string;
-        fields_of_study?: string;
-        open_access_only?: boolean;
-      }) => {
-        const params = new URLSearchParams({
-          query: input.query,
-          limit: String(Math.min(input.limit ?? 10, 100)),
-          fields:
-            "title,abstract,authors,year,citationCount,referenceCount,url,isOpenAccess,openAccessPdf",
-        });
-        if (input.year) params.set("year", input.year);
-        if (input.fields_of_study)
-          params.set("fieldsOfStudy", input.fields_of_study);
-        if (input.open_access_only) params.set("openAccessPdf", "");
-
-        const res = await fetch(`${BASE}/paper/search?${params}`, { headers });
-        if (!res.ok) return toolResult({ error: `API error: ${res.status} ${res.statusText}` });
-        return toolResult(await res.json());
-      },
-    },
-    {
-      name: "get_paper",
-      label: "Get Paper Details (Semantic Scholar)",
-      description:
-        "Get detailed information about a specific paper by its Semantic Scholar ID, DOI, or ArXiv ID.",
-      parameters: Type.Object({
-        paper_id: Type.String({
-          description:
-            "Paper identifier: Semantic Scholar ID, DOI (e.g. '10.1234/...'), or ArXiv ID (e.g. 'arXiv:2301.00001')",
-        }),
-      }),
-      execute: async (input: { paper_id: string }) => {
-        const fields =
-          "title,abstract,authors,year,citationCount,referenceCount,tldr,url,venue,isOpenAccess,openAccessPdf,fieldsOfStudy,publicationDate";
-        const res = await fetch(
-          `${BASE}/paper/${encodeURIComponent(input.paper_id)}?fields=${fields}`,
-          { headers },
-        );
-        if (!res.ok) return toolResult({ error: `API error: ${res.status} ${res.statusText}` });
-        return toolResult(await res.json());
-      },
-    },
-    {
-      name: "get_citations",
-      label: "Get Citations (Semantic Scholar)",
-      description:
-        "Get papers that cite a given paper. Useful for forward citation tracking.",
-      parameters: Type.Object({
-        paper_id: Type.String({ description: "Paper identifier (S2 ID, DOI, or ArXiv ID)" }),
-        limit: Type.Optional(
-          Type.Number({ description: "Max citations to return (default 20, max 100)" }),
-        ),
-        offset: Type.Optional(
-          Type.Number({ description: "Pagination offset" }),
-        ),
-      }),
-      execute: async (input: { paper_id: string; limit?: number; offset?: number }) => {
-        const fields = "title,authors,year,citationCount,url,abstract";
-        const limit = Math.min(input.limit ?? 20, 100);
-        const offset = input.offset ?? 0;
-        const res = await fetch(
-          `${BASE}/paper/${encodeURIComponent(input.paper_id)}/citations?fields=${fields}&limit=${limit}&offset=${offset}`,
-          { headers },
-        );
-        if (!res.ok) return toolResult({ error: `API error: ${res.status} ${res.statusText}` });
-        return toolResult(await res.json());
-      },
-    },
-  ];
-}