dsh-pubmed
Biomedical literature search, open-access PDF retrieval, and knowledge graph tools across PubMed, Europe PMC, OpenAlex, and PubTator3.
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
- Cross-source unified literature search across PubMed, Europe PMC, OpenAlex, and Semantic Scholar with deduplication
- Entity normalization and curated biological relationship lookup with evidence PMIDs via PubTator3
- Structured full-text retrieval from PMC and Europe PMC XML endpoints
- Open-access PDF discovery and local disk downloads aggregated from Unpaywall, Europe PMC, and OpenAlex
- Personal topic-based literature knowledge graph management with Mermaid visualization export
- Citation formatting (APA, MLA, BibTeX, RIS, Vancouver) and identifier conversions (DOI, PMID, PMCID)
Useful For
- Conducting systematic biomedical literature reviews with entity-grounded queries
- Discovering, retrieving, and batch-downloading open-access scientific papers directly within DSH agent workflows
- Constructing and maintaining topic-specific knowledge graphs with curated evidence edges
- Generating standard academic citations and resolving incomplete bibliography identifiers
Who It Fits
- Biomedical and life science researchers
- Medical informatics specialists
- Academic researchers requiring multi-source literature aggregation
- DeepSeek Harness users needing automated paper search and PDF retrieval pipelines
Documented Limitations
- Requires Node.js >= 20 and network access to NCBI, EBI, and Semantic Scholar API endpoints
- Rate limits apply depending on API key configuration (e.g., NCBI API key, Semantic Scholar API key)
- PDF downloads are subject to open-access availability across indexed repositories
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.
package.json declares 1 runtime, 0 development, 2 peer, and 0 optional dependencies.
package.json declares DSH bundle metadata.
GitHub reports the repository license as Apache-2.0.
A root package.json was captured and can be inspected by the registry.
Public GitHub source metadata is available for this registry snapshot.
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
- 0d45f16 · 2026-09-30
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
- 2026-09-30
- Last release
- 2026-09-30
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