--- title: "Literature and database search: papers, patents and sequence records" description: "Biocompile's assistant searches OpenAlex, Semantic Scholar, patents and the web, queries NCBI, Ensembl and ENA, and stores papers you can read and cite." url: https://www.biocompile.com/docs/literature-and-database-search/ section: "Projects and assistant" last_updated: 2026-10-23 --- # Literature and database search: papers, patents and sequence records > Biocompile's assistant searches OpenAlex, Semantic Scholar, patents and the web, queries NCBI, Ensembl and ENA, and stores papers you can read and cite. Source: https://www.biocompile.com/docs/literature-and-database-search/. Index of all Biocompile documentation: https://www.biocompile.com/docs/index.md Biocompile's literature and database search lets the assistant find papers, patents and public sequence records from a plain-language question. It stores the papers it selects with their full text, so you can read, highlight and query them, and every answer cites its sources. ## Search the literature The assistant picks the source that fits the question. These sources are available: - **OpenAlex** for structured scholarly metadata, with filters for year, type, open access and citations, and for retraction status. - **Semantic Scholar** for paper metadata, influential-citation signals and recommendations of related papers. - **Patents, scientific documents and clinical trials**, searched by concept with filters. - **The web**, for package documentation, standards, vendor documents and repositories. Papers are looked up by DOI, PubMed ID, arXiv ID or the source's own identifier. [Agent Skills](https://www.biocompile.com/docs/skills.md) add guides for PubMed, bioRxiv and other literature sources. > Find open-access papers since 2022 on GH11 xylanase thermostability and recommend related work. ## Store and question a paper A stored paper is a paper whose full text Biocompile keeps on the project so it can be cited and queried. When you ask about a specific paper, the assistant stores it and asks targeted questions of the stored text, instead of answering from a search snippet. > Store the paper behind this DOI and tell me which expression host the authors used. The assistant can also read a PDF or a web page it finds, and it keeps the text only when it stores the paper. ## Read a stored paper A stored paper opens as a record with tabs. The labels show a count where they apply. | Tab | What it shows | | --- | --- | | **Overview** | Why the paper is relevant, the abstract, key findings, methods, reagents, key results and conclusions | | **Full Paper** | The full text with a table of contents | | **Figures** | Extracted figures with their captions | | **Tables** | Extracted tables | | **References** | The paper's structured references | | **Highlights** | Your notes and the assistant's, filtered by **All**, **Mine** or **Agent** | | **PDF** | The original PDF | Key findings and methods are marked "AI-extracted from the full paper". The record shows the paper's licence, such as CC BY or CC BY-NC, as a tag. To highlight, select text in the paper, choose **Add note**, write the note and choose **Save**. Biocompile shows "Highlight saved". Edit a comment with **Edit comment** on its card, or remove the highlight with **Delete highlight**. ## Query public databases The assistant queries three public databases through managed tools. | Database | What the assistant can do | | --- | --- | | NCBI Datasets | Resolve gene symbols and IDs, search and summarize genomes, get taxonomy and virus reports, and return sequence download links | | Ensembl | Annotate variants with the Variant Effect Predictor from HGVS notation, identifiers such as rsIDs, or genomic regions, and list assemblies and species | | European Nucleotide Archive | Search studies by keyword, taxon or filters, read study details and linked publications, and list run files with checksums | For ENA files, the assistant generates a download script for you to review. It does not run the script. ## Limitations | What is limited | The limit | What to do instead | | --- | --- | --- | | Variant annotation in one batch | 200 variants | Split larger lists into several requests | | ENA study search | 1,000 records per call | Narrow the search with filters | | NCBI gene and genome download links | 20 IDs or accessions per request | Ask in several requests | | ENA downloads | A script is generated, not run | Review the script, then run it where you need the files | | Full text of a paper | Needs the paper itself or an open-access link | Give the assistant the link or the file | ## Common questions ### Which literature sources does Biocompile search? Biocompile searches OpenAlex, Semantic Scholar, patent and clinical-trial documents, and the web. Agent Skills extend this to PubMed, arXiv, bioRxiv and medRxiv. ### Does the assistant cite what it finds? Yes. The assistant cites the papers and records it uses, and a stored paper keeps its full text on the project so you can check a claim against the source. ### Can I search NCBI or Ensembl from a question? Yes. Ask in plain language, for example for a gene by symbol and taxon or for the consequences of a variant. The assistant calls the NCBI Datasets, Ensembl or ENA tool that fits and reports the result. ## Related - [AI research assistant: ask your files and the literature](https://www.biocompile.com/docs/ai-research-assistant.md) - [Agent Skills: scientific workflows for the AI assistant](https://www.biocompile.com/docs/skills.md) - [Research reports: save cited findings and build on them](https://www.biocompile.com/docs/research-reports.md) ## Get access to Biocompile Biocompile is used in the browser at https://app.biocompile.com. It is free to start and no payment method is required: sign up at https://app.biocompile.com/signup?mc_cta=docs-md&mc_path=/docs/literature-and-database-search.md. If your team already uses Biocompile, ask an organization admin to invite you. Research teams that want hands-on setup can apply for the founder-led pilot at https://www.biocompile.com/pilot/. Questions: https://www.biocompile.com/contact/.