"Using Gemini CLI for research purposes" matching MCP servers:

AI-operable research workspace integrating Zotero, Obsidian, and NotebookLM. Search papers (arXiv/Semantic Scholar/PubMed/CrossRef), ingest into Zotero, sync per-paper notes to Obsidian, verify NotebookLM briefs. All three external tools optional.

45-tool MCP server for video analysis, deep research, content extraction, web search, and Weaviate knowledge storage. Powered by Gemini 3.1 Pro.

CLI and stdio MCP server for noticed. Exposes ~50 noticed agent capabilities (network search across GitHub + LinkedIn, missions, PRM, memory, workspace, web search, cron, ...) via two meta-tools — search + execute — to any MCP-aware client (Claude Code, Claude Desktop, Cursor, ChatGPT).

Enables AI-moderated interviews that become cited, searchable transcripts, with a repository Q&A tool that returns exact transcript quotes.

Enables producing verifiable FORRT nanopublication chains with grounded quote verification and compact Science Live constellation projections, supporting reproduction, replication, and new research workflows.

Enables capturing Claude conversations as Obsidian notes and searching the vault from chat, using the Obsidian CLI.

Empowers coding agents for machine learning research by providing access to Lacuna's research map, including novel research proposals, research directions, papers, authors, venues, institutions, and hypotheses. It enables searching and retrieving context-aware research information through MCP tools.

Persistent project context for Google Gemini. 12 MCP tools for .faf Project DNA — auto-detect your stack, validate, score, and sync across CLAUDE.md, GEMINI.md, and AGENTS.md. Python/FastMCP. IANA-registered format (application/vnd.faf+yaml). 183 tests. One file, every AI platform.

A research assistant server that enables saving, organizing, and retrieving research content with semantic search using ChromaDB and OpenAI embeddings.

Provides MCP tools to search, browse, and retrieve unified read-only history from CLI agents like Codex, Claude Code, and OpenCode, with connector discovery and project-folder grouping.

Enables an agent to capture cited sources with extracted bibliographic metadata, keep linked research notes, and search them all. It turns those into BibTeX, annotated Markdown bibliographies, or themed literature-review outlines, stored as plain files inside the project.

Enables interaction with Obsidian vaults through the official Obsidian CLI, allowing note management, search, and vault operations without plugins or API keys.

A version-aware cache for web research that stores and serves documentation references, preventing models from re-researching the same topics across sessions.

Enables creation and querying of knowledge bases using Google's Gemini API File Search feature, allowing AI applications to upload documents and retrieve information through RAG (Retrieval-Augmented Generation).

An append-only research operations framework and read-only MCP that tracks research plans, approvals, observations, claims, failures, revisions, and contributions with source-grounded evidence, providing search, evidence fetch, and audit capabilities without direct ledger writes.

Enables programmatic control of Obsidian vaults via REST API and MCP server for automation and AI assistant integration.

Bridges CLI tools to AI assistants via MCP, enabling knowledge graph management and file reading capabilities.

Turns a codebase into a persistent knowledge graph so AI coding agents can answer structural questions about functions, call chains, routes, and cross-service links through graph queries instead of reading files one by one.

Connect any AI client to the CaBrain memory system via MCP, exposing tools for memory recall, retain, and brain management.

Enables MCP clients to interact with an Obsidian vault through the official Obsidian CLI, supporting search, notes, tasks, files, links, and native Canvas operations while the Obsidian desktop app is running.