Search literature and write notes into Zotero
With agentic AI tools taking the world by storm, this post explores various academic use cases with Claude Code, an AI assistant developed by Anthropic. Task: With agentic AI tools taking the world by storm, this post explores various academic use cases with Claude Code, an AI assistant developed by Anthropic. We will focus on research tasks such as literature assistance, codebase support, etc. The idea is to use AI as your personal research assistant but not to replace your own thinking and creativity. Note: This post will be updated as I discover new use cases and tools. Check back for the latest additions. Literature Search I usually start my research by doing a literature search on Google Scholar, finding a few interesting papers, and then—based on those papers—searching for other related papers (e.g., papers that have cited them). This is time-consuming and often I find myself getting lost in the sea of papers. With Claude, I can quickly find relevant papers based on a specific topic or keyword using natural language. For example, if I’m interested in “machine learning in hydrology,” I can ask Claude to retrieve relevant papers published in the last 5 years using a prompt like: Claude will search the web including Google Scholar and return a list of relevant papers, including their titles, authors, publication years, and even a brief summary if available. Then, I can further ask Claude to look for papers that have cited these key papers, like a citation graph, to get other relevant papers. Optionally, you can ask Claude to retrieve the PDF or fulltext of the papers if they are accessible. You can then pass those papers to Zotero for management and annotation (see next section). You can even ask Claude to write a literature review based on the retrieved papers, though I haven’t tested that yet. Setup Install the Paper Search MCP. Edit the SKILL.md file to replace the placeholder values <REPO_PATH>. You can also just ask Claude to edit the file for you. Literature Management Search for Relevant Papers in Zotero I find this the most useful feature. I use Zotero to manage my references, and I often struggle to find relevant papers when the library contains hundreds of entries. The search function in Zotero is just not that good. With Claude, I can quickly find papers related to a specific topic or keyword using natural language. For instance, if I’m researching “machine learning in hydrology,” I can ask Claude to retrieve relevant papers from my Zotero library, using a prompt like: Then Claude will return a list of relevant papers, including their titles, authors, publication years, and even a brief summary if available. This saves me a lot of time and helps me stay organized with my research materials. The main benefit of using Zotero is it prevents Claude from hallucinating papers that do not exist. Summarize Research Papers Another great use case is summarizing research papers. I often annotate papers as I read and have developed a color code for different annotation types. When I am done, I export the annotations as notes to my Obsidian app (see my previous post on this workflow). I also like to write a short summary highlighting the key points and knowledge gaps. All of this was done manually, and it can be time-consuming when you have many papers. With Claude, I can quickly generate summaries of papers based on my annotations and let it write the note into Zotero or Obsidian. For example, I can ask: Claude may ask a few clarifying questions about the note. It will then generate a concise summary based on the annotations. When you open Zotero, the note is there. This is especially useful when I want to quickly review the key points of a paper without having to read through the entire document again. It also helps me keep my notes organized and easily accessible for future reference. You can also ask Claude to write a “when to cite” section based on the summary and annotations. Setup Install the Zotero MCP. Enable Zotero Local API: Settings-->Advanced-->Miscellaneous, toggle the box for Allow other applications on this computer to communicate with Zotero. It will say Available at http://localhost:23119/api/ Initialize and Update database. Manage Email Subscription; tools: Claude. Human role: The original post does not say how a person stayed involved.; limitations: Prerequisites include installing specific MCPs, configuring Zotero's local API, and maintaining a clean library. The author warns that AI can hallucinate non-existent papers, mitigated by using Zotero as the source of truth. Integration uncertainty exists regarding the stability of third-party MCPs and the need for manual verification of all AI-generated content..
Tools
Published on Agent Work Atlas:
Overview
With agentic AI tools taking the world by storm, this post explores various academic use cases with Claude Code, an AI assistant developed by Anthropic.
Workflow
With agentic AI tools taking the world by storm, this post explores various academic use cases with Claude Code, an AI assistant developed by Anthropic. We will focus on research tasks such as literature assistance, codebase support, etc. The idea is to use AI as your personal research assistant but not to replace your own thinking and creativity. Note: This post will be updated as I discover new use cases and tools. Check back for the latest additions. Literature Search I usually start my research by doing a literature search on Google Scholar, finding a few interesting papers, and then—based on those papers—searching for other related papers (e.g., papers that have cited them). This is time-consuming and often I find myself getting lost in the sea of papers. With Claude, I can quickly find relevant papers based on a specific topic or keyword using natural language. For example, if I’m interested in “machine learning in hydrology,” I can ask Claude to retrieve relevant papers published in the last 5 years using a prompt like: Claude will search the web including Google Scholar and return a list of relevant papers, including their titles, authors, publication years, and even a brief summary if available. Then, I can further ask Claude to look for papers that have cited these key papers, like a citation graph, to get other relevant papers. Optionally, you can ask Claude to retrieve the PDF or fulltext of the papers if they are accessible. You can then pass those papers to Zotero for management and annotation (see next section). You can even ask Claude to write a literature review based on the retrieved papers, though I haven’t tested that yet. Setup Install the Paper Search MCP. Edit the SKILL.md file to replace the placeholder values <REPO_PATH>. You can also just ask Claude to edit the file for you. Literature Management Search for Relevant Papers in Zotero I find this the most useful feature. I use Zotero to manage my references, and I often struggle to find relevant papers when the library contains hundreds of entries. The search function in Zotero is just not that good. With Claude, I can quickly find papers related to a specific topic or keyword using natural language. For instance, if I’m researching “machine learning in hydrology,” I can ask Claude to retrieve relevant papers from my Zotero library, using a prompt like: Then Claude will return a list of relevant papers, including their titles, authors, publication years, and even a brief summary if available. This saves me a lot of time and helps me stay organized with my research materials. The main benefit of using Zotero is it prevents Claude from hallucinating papers that do not exist. Summarize Research Papers Another great use case is summarizing research papers. I often annotate papers as I read and have developed a color code for different annotation types. When I am done, I export the annotations as notes to my Obsidian app (see my previous post on this workflow). I also like to write a short summary highlighting the key points and knowledge gaps. All of this was done manually, and it can be time-consuming when you have many papers. With Claude, I can quickly generate summaries of papers based on my annotations and let it write the note into Zotero or Obsidian. For example, I can ask: Claude may ask a few clarifying questions about the note. It will then generate a concise summary based on the annotations. When you open Zotero, the note is there. This is especially useful when I want to quickly review the key points of a paper without having to read through the entire document again. It also helps me keep my notes organized and easily accessible for future reference. You can also ask Claude to write a “when to cite” section based on the summary and annotations. Setup Install the Zotero MCP. Enable Zotero Local API: Settings-->Advanced-->Miscellaneous, toggle the box for Allow other applications on this computer to communicate with Zotero. It will say Available at http://localhost:23119/api/ Initialize and Update database. Manage Email Subscription
Reported result
The source reports qualitative benefits like time savings and better organization but provides no measured metrics or failure rates. It explicitly notes that the literature review generation feature was not tested. A measurable acceptance check would be comparing the time taken to find and summarize 10 papers manually versus using the AI workflow.
Human role
The original post does not say how a person stayed involved.
Limitations
Prerequisites include installing specific MCPs, configuring Zotero's local API, and maintaining a clean library. The author warns that AI can hallucinate non-existent papers, mitigated by using Zotero as the source of truth. Integration uncertainty exists regarding the stability of third-party MCPs and the need for manual verification of all AI-generated content.
Try it
Act as a research assistant using Claude Code. I have installed the Paper Search and Zotero MCPs. My Zotero library is at [replaceable path] and contains papers on [replaceable topic]. First, perform a dry run: search for 3 recent papers on [replaceable topic] using the Paper Search MCP. Verify these papers exist in Google Scholar. If valid, import them into Zotero. Next, select one existing paper in my library with annotations. Generate a summary of its key findings and knowledge gaps based on my notes. Do not write to Zotero yet. Show me the proposed summary and the list of imported papers for my approval. Only after I confirm, write the summary note into Zotero. If any paper cannot be verified, stop and report the error. Ensure no hallucinated citations are included.
Source reports are not independently verified. Publication date is the catalog publication date, not the original article date.