dsh-pubmed
PubMed and Europe PMC literature search, metadata, citations, and personal knowledge graph plugin for DeepSeek Harness.
Install
$ dsh plugin --profile web add dsh-pubmed@latestPlugin Overview & Capabilities
AI-assisted organization based on the public repository snapshot. The content must be grounded in source evidence and does not replace compatibility or security verification.
Key Capabilities
- PubMed and Europe PMC literature search with boolean query, date, and field filtering
- Article metadata fetching, PMC JATS full-text retrieval, and ID conversion (PMID, PMCID, DOI)
- Citation generation in APA 7, MLA 9, BibTeX, RIS, and Vancouver formats
- PubTator3 biomedical concept annotation, entity ID lookup, and curated relationship extraction
- Dual-layer literature knowledge graph (session and persistent user scope) with incremental graph merging
- Knowledge graph visualization in Mermaid format with Nature Publishing Group (NPG) color styling
- MeSH vocabulary lookup, citation matching (ECitMatch), and spelling correction
- Automatic request queueing and rate-limit handling with optional NCBI API key support
Useful For
- Conducting automated biomedical literature reviews and PubMed searches in DeepSeek Harness
- Building incremental research knowledge graphs across multiple search queries and sessions
- Generating citation entries and bibliographic metadata for academic writing
- Exploring disease-gene-chemical relationships using PubTator3 curated concept annotations
- Translating between publication identifiers (PMID, PMCID, DOI)
Who It Fits
- Biomedical and life sciences researchers
- Bioinformatics and computational biology practitioners
- Academic researchers and students compiling scientific bibliographies
- AI agent developers building clinical and biomedical workflows in DeepSeek Harness
Documented Limitations
- Requires outbound network access to NCBI (eutils.ncbi.nlm.nih.gov) and Europe PMC (ebi.ac.uk)
- Subject to NCBI rate limits (3 req/s default, 10 req/s with NCBI_API_KEY) and PubTator3 limits (3 req/s)
- Full-text extraction from PMC XML/JATS is best-effort and depends on PMC open-access availability
DSH Compatibility
Version-specific runtime evidence collected by DSH Plugin. A missing result means we have not tested that combination yet.
Security Signals
Objective signals discovered from package metadata and source inspection. These are not a guarantee that a plugin is safe.
Source & Registry Notes
Public provenance, Registry classification, and the latest source check for this entry, kept separate from runtime verification.
- Source repository
- aiyacharley/dsh-pubmed
- Registry source
- GitHub · dsh-plugin topic
- Registry classification
- Plugin
- Source checked
- a50e943 · 2026-09-21
This project is independently indexed from public source information. DSH Plugin is not affiliated with DeepSeek or the plugin author. Always check the author repository before installation.
Repository Activity
- GitHub stars
- 2GitHub stars
- Forks
- 0
- Open issues
- 0
- Last commit
- 2026-09-18
- Last release
- 2026-09-18
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