ATHENA: analysis of tumor heterogeneity from spatial omics measurements.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35485743", "kind": "science-record", "revision": 3, "content_hash": "sha256:37008f7256da0e6e0edabfdef5e64eb279802df76ea2192d0b27841d0aca578a", "created_at": "2026-11-01T18:14:21Z", "updated_at": "2026-11-01T21:27:44Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "ATHENA: analysis of tumor heterogeneity from spatial omics measurements.", "doi": "10.1093/bioinformatics/btac303", "pmid": "35485743", "authors": ["Adriano Luca Martinelli", "Maria Anna Rapsomaniki"], "journal": "Bioinformatics (Oxford, England)", "year": 2022, "abstract": "SUMMARY: Tumor heterogeneity has emerged as a fundamental property of most human cancers, with broad implications for diagnosis and treatment. Recently, spatial omics have enabled spatial tumor profiling, however computational resources that exploit the measurements to quantify tumor heterogeneity in a spatially aware manner are largely missing. We present ATHENA (Analysis of Tumor HEterogeNeity from spAtial omics measurements), a computational framework that facilitates the visualization, processing and analysis of tumor heterogeneity from spatial omics measurements. ATHENA uses graph representations of tumors and bundles together a large collection of established and novel heterogeneity scores that quantify different aspects of the complexity of tumor ecosystems.\nAVAILABILITY AND IMPLEMENTATION: ATHENA is available as a Python package under an open-source license at: https://github.com/AI4SCR/ATHENA. Detailed documentation and step-by-step tutorials with example datasets are also available at: https://ai4scr.github.io/ATHENA/. The data presented in this article are publicly available on Figshare at https://figshare.com/articles/dataset/zurich_pkl/19617642/2.\nSUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.", "claims": [{"id": "claim-method", "statement": "Quantification of local Rao’s quadratic entropy highlights tumor regions with high diversity of interactions between phenotypically distant cells (Fig. 1D).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35485743", "locator": "sections[3] \"3 Results\" paragraph 2", "quote": "Quantification of local Rao’s quadratic entropy highlights tumor regions with high diversity of interactions between phenotypically distant cells (Fig. 1D)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data presented in this article are publicly available on Figshare at https://figshare.com/articles/dataset/zurich_pkl/19617642/2.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35485743", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The data presented in this article are publicly available on Figshare at https://figshare.com/articles/dataset/zurich_pkl/19617642/2."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We present ATHENA (Analysis of Tumor HEterogeNeity from spAtial omics measurements), a computational framework that facilitates the visualization, processing and analysis of tumor heterogeneity from spatial omics measurements.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35485743", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We present ATHENA (Analysis of Tumor HEterogeNeity from spAtial omics measurements), a computational framework that facilitates the visualization, processing and analysis of tumor heterogeneity from spatial omics measurements."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "We present ATHENA (Analysis of Tumor HEterogeNeity from spAtial omics measurements), a computational framework that facilitates the visualization, processing and analysis of tumor heterogeneity from spatial omics measurements.", "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:35485743"], "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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