PloverDB: a high-performance platform for serving biomedical knowledge graphs as standards-compliant web APIs.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40580448", "kind": "science-record", "revision": 1, "content_hash": "sha256:abea6770ae54728326034507947faf2be6af542733225f471d15b0d91bc8f85e", "created_at": "2026-11-01T20:30:40Z", "updated_at": "2026-11-01T20:30:40Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "PloverDB: a high-performance platform for serving biomedical knowledge graphs as standards-compliant web APIs.", "doi": "10.1093/bioinformatics/btaf380", "pmid": "40580448", "authors": ["Amy K Glen", "Eric W Deutsch", "Stephen A Ramsey"], "journal": "Bioinformatics (Oxford, England)", "year": 2025, "abstract": "SUMMARY: Knowledge graphs are increasingly being used to integrate heterogeneous biomedical knowledge and data. General-purpose graph database management systems such as Neo4j are often used to host and search knowledge graphs, but such tools come with overhead and leave biomedical-specific standards compliance and reasoning to the user. Interoperability across biomedical knowledge bases and reasoning systems necessitates the use of standards such as those adopted by the Biomedical Data Translator consortium. We present PloverDB, a comprehensive software platform for hosting and efficiently serving biomedical knowledge graphs as standards-compliant web application programming interfaces. In addition to fundamental back-end knowledge reasoning tasks, PloverDB automatically handles entity resolution, exposure of standardized metadata and test data, and multiplexing of knowledge graphs, all in a single platform designed specifically for efficient query answering and ease of deployment. PloverDB increases data accessibility and utility by allowing data providers to quickly serve their biomedical knowledge graphs as standards-compliant web services.\nAVAILABILITY AND IMPLEMENTATION: PloverDB's source code and technical documentation are publicly available under an MIT License at github:RTXteam/PloverDB, archived on Zenodo at doi:10.5281/zenodo.15454600.", "claims": [{"id": "claim-data-access", "statement": "Supplementary data is available at Bioinformatics online.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40580448", "locator": "sections[14] \"Supplementary data\" paragraph 2", "quote": "Supplementary data is available at Bioinformatics online."}], "state": "complete"}, {"id": "claim-target-result", "statement": "PloverDB was 14-times faster than Plater on average across the 51 randomly selected queries for which the two platforms returned identical answer sets.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40580448", "locator": "sections[7] \"2.1.4 Performance\" paragraph 5", "quote": "PloverDB was 14-times faster than Plater on average across the 51 randomly selected queries for which the two platforms returned identical answer sets (Table 1, available as supplementary data at Bioinformatics online)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "PloverDB was 14-times faster than Plater on average across the 51 randomly selected queries for which the two platforms returned identical answer sets.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:40580448"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["Supplementary data is available at Bioinformatics online."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:40580448"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:55:00Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 6725, "completion_tokens": 549, "cached_tokens": 128}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:40580448", "type": "paper", "label": "pmid:40580448"}, {"id": "source:pmid:40580448", "type": "manuscript", "label": "PMID 40580448 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40580448", "type": "paper", "label": "pmid:40580448"}, {"id": "source:pmid:40580448", "type": "manuscript", "label": "PMID 40580448 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40580448", "type": "extraction", "used": ["source:pmid:40580448"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": null, "parent_hash": null, "fork_of": null, "generation": 0}, "gaps": ["execution.not_run", "method", "operations", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"]}