About Pubtator Link
Pubtator Link is an MCP server in the Healthcare category: mCP server for NCBI PubTator3: biomedical literature search with gene, variant, disease and chemical entity annotation — returns compact, citable passages instead of raw BioC.
Install
git clone https://github.com/berntpopp/pubtator-linkThis server has no ConduID identity, so agent calls to it are not receipted. Pin the version you install and review the source before granting it credentials.
Tools (35)
build_topic_literature_mapBounded topic map across papers, authors, citations, and entities
Parameters not published.
convert_article_idsNormalize PMIDs, PMCIDs, and DOIs to candidate PMIDs
Parameters not published.
diagnosticsSubsystem status and recovery commands
Parameters not published.
estimate_publication_contextEstimate passage count and context size before fetching
Parameters not published.
find_entity_relationsLiterature-derived related entities for a PubTator entity
Parameters not published.
find_related_articlesSimilar, cited-by, or reference-linked articles for seed PMIDs
Parameters not published.
find_related_evidence_candidatesFull-text-preferred related candidates for one seed PMID
Parameters not published.
get_citationCandidate PMIDs from a free-text citation
Parameters not published.
get_evidence_certaintyOne user-supplied evidence-certainty judgment
Parameters not published.
get_meshMeSH descriptors and candidate PubMed search terms
Parameters not published.
Show all 35 tools
get_neighboring_review_passagesPrepared passages adjacent to a cited passage, for local context
Parameters not published.
get_pmc_annotationsRaw full-text BioC annotation export for PMC IDs
Parameters not published.
get_publication_annotationsRaw PubTator BioC annotation export for PMIDs
Parameters not published.
get_publication_citation_graphReference and cited-by neighbours for one publication
Parameters not published.
get_publication_metadataCitation-grade metadata for known PMIDs
Parameters not published.
get_publication_passagesCompact citable passages for PMIDs, without raw BioC
Parameters not published.
get_research_session_statusStaged candidate, coverage, and preparation status
Parameters not published.
get_review_audit_trailCopy-ready audit block for selected prepared passages
Parameters not published.
get_review_contextCompact citable context from prepared review passages
Parameters not published.
get_review_context_batchPreferred retrieval path: merges several query variants in one call
Parameters not published.
get_review_index_summaryOne persisted review index summary, without passage samples
Parameters not published.
get_review_passages_by_idExact prepared review passages by stable passage ID
Parameters not published.
get_server_capabilitiesSupported tools, transports, formats, and limitations
Parameters not published.
get_text_annotation_resultsResults for an asynchronous text-annotation session
Parameters not published.
get_variant_evidenceExact/equivalent source classifications, distinct from non-classifying candidates
Parameters not published.
inspect_review_indexIndexed PMIDs, sections, passage counts, and failures for a `review_id`
Parameters not published.
list_evidence_certaintyUser-supplied evidence-certainty judgments for a review
Parameters not published.
list_research_sessionsCompact cursor-paginated session summaries; status provides details
Parameters not published.
list_review_indexesPersisted review indexes with status, counts, and storage size
Parameters not published.
preflight_review_sourcesSource coverage and full-text vs abstract-only outlook before indexing
Parameters not published.
search_biomedical_entitiesCanonical PubTator entity IDs (gene, disease, chemical, species, variant, cell line)
Parameters not published.
search_guidelinesGuideline, consensus, and systematic-review papers
Parameters not published.
search_literaturePubMed literature search through PubTator3
Parameters not published.
suggest_corpusCompact review-feeding candidate PMID corpus for a question
Parameters not published.
workflow_helpCanonical research workflow for a fresh context
Parameters not published.
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