{ "release_id": "2026-09-30-e37e3ab1284d", "released_at": "2026-09-30T21:54:42.169287Z", "scope": "Every published benchmark, task, protocol and evaluator page; counts use reviewed membership links and exclude private submissions.", "summary": { "benchmark": { "pages": 51, "with_results": 50, "with_charts": 38 }, "task": { "pages": 495, "with_results": 473, "with_charts": 389 }, "protocol": { "pages": 406, "with_results": 399, "with_charts": 326 }, "evaluator": { "pages": 4, "with_results": 0, "with_charts": 0 } }, "pages": [ { "id": "discovery-benchmark-atom3d", "kind": "benchmark", "name": "ATOM3D", "status": "discovered", "url": "/database/benchmark/discovery-benchmark-atom3d/", "evaluations": 57, "metric_rows": 57, "charts": 14, "charted_metric_rows": 57, "chart_protocol_ids": [ "atom3d-task-lba-rmse", "atom3d-task-lba-rp", "atom3d-task-lba-rs", "atom3d-task-lep-auroc", "atom3d-task-msp", "atom3d-task-pip", "atom3d-task-psr-global-rs", "atom3d-task-psr-mean-rs", "atom3d-task-res", "atom3d-task-rsr-global-rs", "atom3d-task-rsr-mean-rs", "atom3d-task-smp-egap", "atom3d-task-smp-mu", "atom3d-task-smp-u0at" ], "state": "charts_available", "source_ids": [ "src-discovery-drorlab-atom3d", "evidence-expansion-atom3d-92656c20", "run-doc-atom3d-readme-md-4c2f3b7e", "project-recipe-atom3d-4c2f3b7e", "evidence-discovery-final-atom3d" ], "source_urls": [ "https://github.com/drorlab/atom3d/blob/4c2f3b7e9efe128791b83f03b2e8cae91e78b018/README.md", "https://arxiv.org/pdf/2012.04035v4", "https://github.com/drorlab/atom3d/blob/4c2f3b7e9efe128791b83f03b2e8cae91e78b018/README.md", "https://github.com/drorlab/atom3d/blob/4c2f3b7e9efe128791b83f03b2e8cae91e78b018/README.md", "https://arxiv.org/abs/2012.04035v4" ], "research_status": "primary_protocol_reviewed", "research_review_date": "2026-09-17", "gaps": [ "complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows." ] }, { "id": "discovery-benchmark-beacon", "kind": "benchmark", "name": "BEACON", "status": "discovered", "url": "/database/benchmark/discovery-benchmark-beacon/", "evaluations": 221, "metric_rows": 221, "charts": 13, "charted_metric_rows": 221, "chart_protocol_ids": [ "beacon-task-apa", "beacon-task-cmp", "beacon-task-cri-off", "beacon-task-cri-on", "beacon-task-dmp", "beacon-task-modif", "beacon-task-mrl", "beacon-task-ncrna", "beacon-task-prs", "beacon-task-spl", "beacon-task-ssi", "beacon-task-ssp", "beacon-task-vdp" ], "state": "charts_available", "source_ids": [ "src-discovery-terry-r123-rnabenchmark", "evidence-expansion-p2-evidence-discovery-final-beacon-c2496bff164b", "run-doc-beacon-readme-md-da7f9c7a", "project-recipe-beacon-da7f9c7a", "evidence-discovery-final-beacon" ], "source_urls": [ "https://github.com/terry-r123/RNABenchmark/blob/da7f9c7ac3f39605af27e1dfcdf879adba963d79/README.md", "https://arxiv.org/pdf/2406.10391v1", "https://github.com/terry-r123/RNABenchmark/blob/da7f9c7ac3f39605af27e1dfcdf879adba963d79/README.md", "https://github.com/terry-r123/RNABenchmark/blob/da7f9c7ac3f39605af27e1dfcdf879adba963d79/README.md", "https://arxiv.org/pdf/2406.10391v1" ], "research_status": "source_found_structured_extraction_pending", "research_review_date": "2026-09-17", "gaps": [ "Multi-task suite; model adaptation and metric differ by task. Full comparison table extraction remains pending; no composite RNA score inferred." ] }, { "id": "discovery-benchmark-beeline", "kind": "benchmark", "name": "BEELINE", "status": "discovered", "url": "/database/benchmark/discovery-benchmark-beeline/", "evaluations": 384, "metric_rows": 588, "charts": 71, "charted_metric_rows": 588, "chart_protocol_ids": [ "acquired-protocol-024f47659eb7e75f56dc", "acquired-protocol-1227fd691dca8a3aa41d", "acquired-protocol-174f1a5acdc3c13db7b2", "acquired-protocol-18da78ff7de51ffb5605", "acquired-protocol-19f8c76e99a986094a6f", "acquired-protocol-1b09d04bdd84c0554bd1", "acquired-protocol-25210daa0dccd840d2fb", "acquired-protocol-2a8b0faaeabb2b42f8fb", "acquired-protocol-30ca92be5250d3347718", "acquired-protocol-34109c3e92506dce8489", "acquired-protocol-37b5599b7d976211e8c1", "acquired-protocol-3c4df1f88f28c01a7508", "acquired-protocol-408cb9c598ef659f51a6", "acquired-protocol-4178cb595371e239c8fd", "acquired-protocol-4745597f348c3ff0e85a", "acquired-protocol-51354be75f1492ed099a", "acquired-protocol-562a238b609a61077d81", "acquired-protocol-61ae01473c4e5c4a9ce5", "acquired-protocol-6ddc5a89a2b4c4c474d7", "acquired-protocol-78f8093a50e8fca5eacc", "acquired-protocol-7913b13aba9d987c38ae", "acquired-protocol-7977f5aa02ec0001bc1a", "acquired-protocol-7f7b37c767904dd8a6fb", "acquired-protocol-81fdcee5288c3672584a", "acquired-protocol-994c136cc78955a7777e", "acquired-protocol-a72274bbb664040489be", "acquired-protocol-a8f87266d6be53bbd23b", "acquired-protocol-a930238c7acc35fd34ee", "acquired-protocol-a9a52bfc61cc00ae40eb", "acquired-protocol-b022aafcf374cd51f0f3", "acquired-protocol-b1b289fa63273aa8bba2", "acquired-protocol-b3a78798ab8a7602a63a", "acquired-protocol-b614e3405917763fb159", "acquired-protocol-b782c1901e3d8fb8348e", "acquired-protocol-b7da29c68a46720cce0b", "acquired-protocol-bd571aa3305cceba1f0b", "acquired-protocol-bd9b01304308808a7b38", "acquired-protocol-c57e646de930422fa536", "acquired-protocol-c7f45d872952b996c96a", "acquired-protocol-c8cff8ffd3fbf524bf2e", "acquired-protocol-ceaaa7b9d8af61e51736", "acquired-protocol-d60261afa2c58e4aa12e", "acquired-protocol-d66bbf2b3dd743f2db47", "acquired-protocol-dc2ce864a7578927cabc", "acquired-protocol-e0ffaca06ad1222ac21e", "acquired-protocol-eceec78306355eece4e7", "acquired-protocol-ed61833eb749ba711c5b", "acquired-protocol-edb7d264956f89df17fc", "acquired-protocol-f4f5a4cb785dc55503bb", "acquired-protocol-f6bd2f323f0f81692075", "acquired-protocol-f6bf921e477601ffffec", "acquired-protocol-f7ef0c77a6155a1ff0d4", "acquired-protocol-fabd886c5f7a9dbfdbab", "acquired-protocol-fbb04bf73e09481732c8" ], "state": "charts_available", "source_ids": [ "src-discovery-murali-group-beeline", "expansion-p3-beeline", "run-doc-beeline-readme-md-37464085", "run-doc-beeline-config-yaml-37464085", "evidence-discovery-final-beeline" ], "source_urls": [ "https://github.com/Murali-group/Beeline/blob/37464085eb8a95d6cc6a3d3a3c649d36db6052ed/README.md", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC7098173/fullTextXML", "https://github.com/Murali-group/Beeline/blob/37464085eb8a95d6cc6a3d3a3c649d36db6052ed/README.md", "https://github.com/Murali-group/Beeline/blob/37464085eb8a95d6cc6a3d3a3c649d36db6052ed/config-files/config.yaml", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC7098173/fullTextXML" ], "research_status": "primary_figures_located", "research_review_date": "2026-09-17", "gaps": [ "Primary XML has no numeric table-wrap results; comparisons are figures and supplementary data. Exact full model-by-dataset scores require supplemental/source-data extraction, not digitizing figure heights." ] }, { "id": "discovery-benchmark-bend", "kind": "benchmark", "name": "BEND", "status": "discovered", "url": "/database/benchmark/discovery-benchmark-bend/", "evaluations": 105, "metric_rows": 105, "charts": 7, "charted_metric_rows": 105, "chart_protocol_ids": [ "bend-task-chromatin", "bend-task-cpg", "bend-task-enhancer", "bend-task-gene-finding", "bend-task-histone", "bend-task-variant-disease", "bend-task-variant-expression" ], "state": "charts_available", "source_ids": [ "src-discovery-frederikkemarin-bend", "evidence-expansion-bend-final-f709b6be", "run-doc-bend-readme-md-ac6e80c7", "project-recipe-bend-ac6e80c7", "evidence-discovery-final-bend" ], "source_urls": [ "https://github.com/frederikkemarin/BEND/blob/ac6e80c75e09d83cf47a7b4bcf0e44599c5706cf/README.md", "https://proceedings.iclr.cc/paper_files/paper/2024/file/429e7b31625a8b7839f9e4d6e2aa9bb9-Paper-Conference.pdf", "https://github.com/frederikkemarin/BEND/blob/ac6e80c75e09d83cf47a7b4bcf0e44599c5706cf/README.md", "https://github.com/frederikkemarin/BEND/blob/ac6e80c75e09d83cf47a7b4bcf0e44599c5706cf/README.md", "https://arxiv.org/pdf/2311.12570v1" ], "research_status": "primary_protocol_reviewed", "research_review_date": "2026-09-17", "gaps": [ "complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows." ] }, { "id": "discovery-benchmark-cafa", "kind": "benchmark", "name": "CAFA", "status": "discovered", "url": "/database/benchmark/discovery-benchmark-cafa/", "evaluations": 438, "metric_rows": 438, "charts": 6, "charted_metric_rows": 438, "chart_protocol_ids": [ "acquired-protocol-0841c618c0a89fa56f63", "acquired-protocol-906c90560bda45e6b1af", "acquired-protocol-a8ac152e52ee3e06387c" ], "state": "charts_available", "source_ids": [ "src-discovery-cafa", "evidence-expansion-p2-evidence-discovery-final-cafa3-3802f37548d7", "evidence-benchmark-cafa-20260916", "run-doc-cafa-evaluator-readme-md-d09ba823", "evidence-discovery-final-cafa3" ], "source_urls": [ "https://biofunctionprediction.org/cafa/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC6864930/fullTextXML", "https://biofunctionprediction.org/cafa/", "https://github.com/BioComputingUP/CAFA-evaluator/blob/d09ba823b15d4e8a57cd1311c73e5fec3ef1c035/README.md", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC6864930/fullTextXML" ], "research_status": "source_found_structured_extraction_pending", "research_review_date": "2026-09-17", "gaps": [ "Main tables describe participation and benchmark construction; numerical performance is mainly in figures/supplementary files. CAFA versions, ontology branch, full/partial mode and no/limited-knowledge cohorts must remain separate. No scores estimated from plot pixels." ] }, { "id": "discovery-benchmark-cami", "kind": "benchmark", "name": "CAMI", "status": "discovered", "url": "/database/benchmark/discovery-benchmark-cami/", "evaluations": 16, "metric_rows": 256, "charts": 16, "charted_metric_rows": 256, "chart_protocol_ids": [ "acquired-protocol-f443b5fdaee9129f2b7a" ], "state": "charts_available", "source_ids": [ "src-discovery-cami", "evidence-expansion-p2-evidence-discovery-final-cami2-da932c1cde8b", "evidence-benchmark-cami-snapshot", "run-doc-cami-official-20260917", "evidence-discovery-final-cami2" ], "source_urls": [ "https://cami-challenge.org/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9007738/fullTextXML", "https://cami-challenge.org/", "https://cami-challenge.org/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9007738/fullTextXML" ], "research_status": "source_found_structured_extraction_pending", "research_review_date": "2026-09-17", "gaps": [ "Main Table 1 gives best-ranked software, not a complete numerical score table. Assembly, genome binning, taxonomic binning and taxonomic profiling are separate tasks; strain diversity and sample cohorts must be separated. Further source-data extraction remains before new score publication." ] }, { "id": "ucc-research-benchmark-cppc", "kind": "benchmark", "name": "Cancer Immunotherapy Data Science Challenge", "status": "source_checked", "url": "/database/benchmark/ucc-research-benchmark-cppc/", "evaluations": 54, "metric_rows": 54, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "ucc-research-source-challenge-paper", "ucc-research-source-challenge-code", "ucc-research-source-challenge-supp-s2" ], "source_urls": [ "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13228547/fullTextXML", "https://raw.githubusercontent.com/uhlerlab/cancer_immunotherapy_data_science_challenge/283328a9b8afc6e882eeb503ac4710bbe9f37371/README.md", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13228547/supplementaryFiles" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "discovery-benchmark-capri", "kind": "benchmark", "name": "CAPRI", "status": "discovered", "url": "/database/benchmark/discovery-benchmark-capri/", "evaluations": 100, "metric_rows": 400, "charts": 16, "charted_metric_rows": 400, "chart_protocol_ids": [ "acquired-protocol-287b8fe8904985b6e420", "acquired-protocol-95bb2d71a1d51316f506", "acquired-protocol-cedd42f89ef2860a1fc7", "acquired-protocol-e7121a74a668c30652c8" ], "state": "charts_available", "source_ids": [ "src-discovery-capri", "expansion-p3-capri-assessment", "evidence-benchmark-capri-snapshot", "run-doc-capri-official-20260917", "evidence-discovery-final-capri", "evidence-discovery-final-dockq" ], "source_urls": [ "https://www.capri-docking.org/", "https://www.capri-docking.org/assessment/", "https://www.capri-docking.org/", "https://www.capri-docking.org/", "https://www.capri-docking.org/assessment/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC4999177/fullTextXML" ], "research_status": "primary_assessment_located_paper_access_blocked", "research_review_date": "2026-09-17", "gaps": [ "Round 54 has 37 targets and 38 assessment units; round 57 has 34 targets and 47 units. These are different denominators.", "Official page says data may change; pin each round CSV before numerical ingestion.", "Freshly discovered Rosetta CAPRI rounds 47–55 paper (PMC12462888) was blocked: Europe PMC HTTP 500 and PMC browser challenge. It is not a universal all-participant assessment." ] }, { "id": "discovery-benchmark-casp", "kind": "benchmark", "name": "CASP", "status": "discovered", "url": "/database/benchmark/discovery-benchmark-casp/", "evaluations": 90, "metric_rows": 270, "charts": 6, "charted_metric_rows": 270, "chart_protocol_ids": [ "acquired-protocol-8068932c1a23c9c3f049" ], "state": "charts_available", "source_ids": [ "src-discovery-casp", "evidence-expansion-casp16-32ef3bdf", "evidence-benchmark-casp-snapshot", "run-doc-casp-official-20260917", "evidence-discovery-final-casp16" ], "source_urls": [ "https://predictioncenter.org/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12750037/fullTextXML", "https://predictioncenter.org/", "https://predictioncenter.org/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12750037/fullTextXML" ], "research_status": "primary_protocol_reviewed", "research_review_date": "2026-09-17", "gaps": [ "complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows." ] }, { "id": "uc-clinical-20260930-benchmark-civic-study", "kind": "benchmark", "name": "CIViC MCP 2026 evidence-retrieval evaluation", "status": "source_checked", "url": "/database/benchmark/uc-clinical-20260930-benchmark-civic-study/", "evaluations": 3, "metric_rows": 162, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "uc-clinical-20260930-source-civic", "uc-clinical-20260930-source-civic-supp" ], "source_urls": [ "https://academic.oup.com/bioinformaticsadvances/article/6/1/vbag209/8746878", "https://academic.oup.com/bioinformaticsadvances/article/6/1/vbag209/8746878#supplementary-data" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "ucc-docking-cluspro-bm5-2020-benchmark", "kind": "benchmark", "name": "ClusPro Protein Docking Benchmark 5.0 study", "status": "source_checked", "url": "/database/benchmark/ucc-docking-cluspro-bm5-2020-benchmark/", "evaluations": 16, "metric_rows": 111, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "ucc-docking-cluspro-bm5-2020-source" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC7484347/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "discovery-benchmark-dart-eval", "kind": "benchmark", "name": "DART-Eval", "status": "discovered", "url": "/database/benchmark/discovery-benchmark-dart-eval/", "evaluations": 316, "metric_rows": 316, "charts": 23, "charted_metric_rows": 316, "chart_protocol_ids": [ "dart-eval-task-ca-auroc-gm12878", "dart-eval-task-ca-auroc-h1esc", "dart-eval-task-ca-auroc-hepg2", "dart-eval-task-ca-auroc-imr90", "dart-eval-task-ca-auroc-k562", "dart-eval-task-ca-spearman-gm12878", "dart-eval-task-ca-spearman-h1esc", "dart-eval-task-ca-spearman-hepg2", "dart-eval-task-ca-spearman-imr90", "dart-eval-task-ca-spearman-k562", "dart-eval-task-cts-acc", "dart-eval-task-cts-gm12878", "dart-eval-task-cts-h1esc", "dart-eval-task-cts-hepg2", "dart-eval-task-cts-imr90", "dart-eval-task-cts-k562", "dart-eval-task-rei-abs", "dart-eval-task-rei-acc", "dart-eval-task-rei-pair", "dart-eval-task-vs-african-auroc", "dart-eval-task-vs-african-pearson-r", "dart-eval-task-vs-yoruban-auroc", "dart-eval-task-vs-yoruban-pearson-r" ], "state": "charts_available", "source_ids": [ "src-discovery-kundajelab-dart-eval", "evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55", "run-doc-dart-eval-readme-md-af2a86d6", "project-recipe-dart-eval-af2a86d6", "runner-04-docs-sdk-md", "runner-04-docs-hpc-md", "runner-04-docs-dart-eval-md", "runner-04-packages-rewirebench-src-rewirebench-protocols-dart-eval-py", "runner-04-packages-rewirebench-src-rewirebench-resources-dart-eval-sources-json", "runner-04-packages-rewirebench-src-rewirebench-resources-dart-eval-statistical-reference-json", "evidence-discovery-final-dart" ], "source_urls": [ "https://github.com/kundajelab/DART-Eval/blob/af2a86d666c35304257c2fa7e15180e1fbcabb01/README.md", "https://arxiv.org/html/2412.05430v1", "https://github.com/kundajelab/DART-Eval/blob/af2a86d666c35304257c2fa7e15180e1fbcabb01/README.md", "https://github.com/kundajelab/DART-Eval/blob/af2a86d666c35304257c2fa7e15180e1fbcabb01/README.md", "https://github.com/rewire-bio/rewire-benchmarks/blob/fcccbbcdbe3d5cd64a1a312d536615273320f7b4/docs/sdk.md", "https://github.com/rewire-bio/rewire-benchmarks/blob/fcccbbcdbe3d5cd64a1a312d536615273320f7b4/docs/hpc.md", "https://github.com/rewire-bio/rewire-benchmarks/blob/fcccbbcdbe3d5cd64a1a312d536615273320f7b4/docs/dart-eval.md", "https://github.com/rewire-bio/rewire-benchmarks/blob/fcccbbcdbe3d5cd64a1a312d536615273320f7b4/packages/rewirebench/src/rewirebench/protocols/dart_eval.py", "https://github.com/rewire-bio/rewire-benchmarks/blob/fcccbbcdbe3d5cd64a1a312d536615273320f7b4/packages/rewirebench/src/rewirebench/resources/dart_eval/sources.json", "https://github.com/rewire-bio/rewire-benchmarks/blob/fcccbbcdbe3d5cd64a1a312d536615273320f7b4/packages/rewirebench/src/rewirebench/resources/dart_eval/statistical-reference.json", "https://arxiv.org/html/2412.05430v1" ], "research_status": "source_found_structured_extraction_pending", "research_review_date": "2026-09-17", "gaps": [ "Regulatory sequence detection, TF motifs, cell-type activity and variant effects are distinct protocols. 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exact discrepancy.", "Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked.", "Subsequent studies use different datasets and are not pooled with this paper." ] }, { "id": "paper-protocol-e8a1aa302bb8df1efd", "kind": "protocol", "name": "ArchiveII (RNA secondary structure)", "status": "needs_review", "url": "/database/protocol/paper-protocol-e8a1aa302bb8df1efd/", "evaluations": 10, "metric_rows": 40, "charts": 4, "charted_metric_rows": 40, "chart_protocol_ids": [ "paper-protocol-e8a1aa302bb8df1efd" ], "state": "charts_available", "source_ids": [ "bpfold-2025" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12216785/" ], "research_status": "complete_tables_extracted", "research_review_date": "2026-09-17", "gaps": [ "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "alphagenome-2026-t3-protocol-16", "kind": "protocol", "name": "ATAC prediction on held-out peaks (AlphaGenome paper)", "status": "needs_review", "url": "/database/protocol/alphagenome-2026-t3-protocol-16/", "evaluations": 2, "metric_rows": 6, "charts": 3, "charted_metric_rows": 6, "chart_protocol_ids": [ "alphagenome-2026-t3-protocol-16" ], "state": "charts_available", "source_ids": [ "source-alphagenome-nature2026-tables", "source-alphagenome-nature2026-supplementary-methods", "evidence-official-56e5abfb5f12f1cd3b20" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-025-10014-0/MediaObjects/41586_2025_10014_MOESM3_ESM.xlsx", "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-025-10014-0/MediaObjects/41586_2025_10014_MOESM1_ESM.pdf", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12851941/" ], "research_status": "complete_comparison_extracted", "research_review_date": "2026-09-17", "gaps": [ "Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked.", "Subsequent studies use different datasets and are not pooled with this paper." ] }, { "id": "alphagenome-2026-t3-protocol-18", "kind": "protocol", "name": "ATAC track prediction at 128 bp (AlphaGenome paper)", "status": "needs_review", "url": "/database/protocol/alphagenome-2026-t3-protocol-18/", "evaluations": 3, "metric_rows": 3, "charts": 1, "charted_metric_rows": 3, "chart_protocol_ids": [ "alphagenome-2026-t3-protocol-18" ], "state": "charts_available", "source_ids": [ "source-alphagenome-nature2026-tables", "source-alphagenome-nature2026-supplementary-methods", "evidence-official-56e5abfb5f12f1cd3b20" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-025-10014-0/MediaObjects/41586_2025_10014_MOESM3_ESM.xlsx", "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-025-10014-0/MediaObjects/41586_2025_10014_MOESM1_ESM.pdf", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12851941/" ], "research_status": "complete_comparison_extracted", "research_review_date": "2026-09-17", "gaps": [ "Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked.", "Subsequent studies use different datasets and are not pooled with this paper." ] }, { "id": "alphagenome-2026-t3-protocol-17", "kind": "protocol", "name": "ATAC track prediction at 32 bp (AlphaGenome paper)", "status": "needs_review", "url": "/database/protocol/alphagenome-2026-t3-protocol-17/", "evaluations": 2, "metric_rows": 2, "charts": 1, "charted_metric_rows": 2, "chart_protocol_ids": [ "alphagenome-2026-t3-protocol-17" ], "state": "charts_available", "source_ids": [ "source-alphagenome-nature2026-tables", "source-alphagenome-nature2026-supplementary-methods", "evidence-official-56e5abfb5f12f1cd3b20" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-025-10014-0/MediaObjects/41586_2025_10014_MOESM3_ESM.xlsx", "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-025-10014-0/MediaObjects/41586_2025_10014_MOESM1_ESM.pdf", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12851941/" ], "research_status": "complete_comparison_extracted", "research_review_date": "2026-09-17", "gaps": [ "Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked.", "Subsequent studies use different datasets and are not pooled with this paper." ] }, { "id": "alphagenome-2026-t4-protocol-7", "kind": "protocol", "name": "Author MFASS splice-disruption prediction (AlphaGenome paper)", "status": "needs_review", "url": "/database/protocol/alphagenome-2026-t4-protocol-7/", "evaluations": 2, "metric_rows": 2, "charts": 1, "charted_metric_rows": 2, "chart_protocol_ids": [ "alphagenome-2026-t4-protocol-7" ], "state": "charts_available", "source_ids": [ "source-alphagenome-nature2026-tables", "source-alphagenome-nature2026-supplementary-methods", "evidence-official-56e5abfb5f12f1cd3b20" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-025-10014-0/MediaObjects/41586_2025_10014_MOESM3_ESM.xlsx", "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-025-10014-0/MediaObjects/41586_2025_10014_MOESM1_ESM.pdf", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12851941/" ], "research_status": "complete_comparison_extracted", "research_review_date": "2026-09-17", "gaps": [ "Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked.", "Subsequent studies use different datasets and are not pooled with this paper." ] }, { "id": "alphagenome-2026-t3-protocol-5", "kind": "protocol", "name": "Base-resolution RNA-seq prediction (AlphaGenome paper)", "status": "needs_review", "url": "/database/protocol/alphagenome-2026-t3-protocol-5/", "evaluations": 2, "metric_rows": 4, "charts": 2, "charted_metric_rows": 4, "chart_protocol_ids": [ "alphagenome-2026-t3-protocol-5" ], "state": "charts_available", "source_ids": [ "source-alphagenome-nature2026-tables", "source-alphagenome-nature2026-supplementary-methods", "evidence-official-56e5abfb5f12f1cd3b20" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-025-10014-0/MediaObjects/41586_2025_10014_MOESM3_ESM.xlsx", "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-025-10014-0/MediaObjects/41586_2025_10014_MOESM1_ESM.pdf", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12851941/" ], "research_status": "complete_comparison_extracted", "research_review_date": "2026-09-17", "gaps": [ "Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked.", "Subsequent studies use different datasets and are not pooled with this paper." ] }, { "id": "acquired-protocol-fabd886c5f7a9dbfdbab", "kind": "protocol", "name": "BEELINE 2020 Figure 2 · BF · {}", "status": "discovered", "url": "/database/protocol/acquired-protocol-fabd886c5f7a9dbfdbab/", "evaluations": 12, "metric_rows": 24, "charts": 2, "charted_metric_rows": 24, "chart_protocol_ids": [ "acquired-protocol-fabd886c5f7a9dbfdbab" ], "state": "charts_available", "source_ids": [ "acquired-source-0f6c059ffdc338b70a5c" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM12_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-562a238b609a61077d81", "kind": "protocol", "name": "BEELINE 2020 Figure 2 · BFC · {}", "status": "discovered", "url": "/database/protocol/acquired-protocol-562a238b609a61077d81/", "evaluations": 12, "metric_rows": 24, "charts": 2, "charted_metric_rows": 24, "chart_protocol_ids": [ "acquired-protocol-562a238b609a61077d81" ], "state": "charts_available", "source_ids": [ "acquired-source-0f6c059ffdc338b70a5c" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM12_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-1b09d04bdd84c0554bd1", "kind": "protocol", "name": "BEELINE 2020 Figure 2 · CY · {}", "status": "discovered", "url": "/database/protocol/acquired-protocol-1b09d04bdd84c0554bd1/", "evaluations": 12, "metric_rows": 24, "charts": 2, "charted_metric_rows": 24, "chart_protocol_ids": [ "acquired-protocol-1b09d04bdd84c0554bd1" ], "state": "charts_available", "source_ids": [ "acquired-source-0f6c059ffdc338b70a5c" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM12_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-18da78ff7de51ffb5605", "kind": "protocol", "name": "BEELINE 2020 Figure 2 · LI · {}", "status": "discovered", "url": "/database/protocol/acquired-protocol-18da78ff7de51ffb5605/", "evaluations": 12, "metric_rows": 24, "charts": 2, "charted_metric_rows": 24, "chart_protocol_ids": [ "acquired-protocol-18da78ff7de51ffb5605" ], "state": "charts_available", "source_ids": [ "acquired-source-0f6c059ffdc338b70a5c" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM12_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-d66bbf2b3dd743f2db47", "kind": "protocol", "name": "BEELINE 2020 Figure 2 · LL · {}", "status": "discovered", "url": "/database/protocol/acquired-protocol-d66bbf2b3dd743f2db47/", "evaluations": 12, "metric_rows": 24, "charts": 2, "charted_metric_rows": 24, "chart_protocol_ids": [ "acquired-protocol-d66bbf2b3dd743f2db47" ], "state": "charts_available", "source_ids": [ "acquired-source-0f6c059ffdc338b70a5c" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM12_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-19f8c76e99a986094a6f", "kind": "protocol", "name": "BEELINE 2020 Figure 2 · TF · {}", "status": "discovered", "url": "/database/protocol/acquired-protocol-19f8c76e99a986094a6f/", "evaluations": 12, "metric_rows": 24, "charts": 2, "charted_metric_rows": 24, "chart_protocol_ids": [ "acquired-protocol-19f8c76e99a986094a6f" ], "state": "charts_available", "source_ids": [ "acquired-source-0f6c059ffdc338b70a5c" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM12_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-25210daa0dccd840d2fb", "kind": "protocol", "name": "BEELINE 2020 Figure 4 · GSD · {}", "status": "discovered", "url": "/database/protocol/acquired-protocol-25210daa0dccd840d2fb/", "evaluations": 12, "metric_rows": 48, "charts": 4, "charted_metric_rows": 48, "chart_protocol_ids": [ "acquired-protocol-25210daa0dccd840d2fb" ], "state": "charts_available", "source_ids": [ "acquired-source-3156602fda847ae943b4" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM13_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-c7f45d872952b996c96a", "kind": "protocol", "name": "BEELINE 2020 Figure 4 · HSC · {}", "status": "discovered", "url": "/database/protocol/acquired-protocol-c7f45d872952b996c96a/", "evaluations": 12, "metric_rows": 48, "charts": 4, "charted_metric_rows": 48, "chart_protocol_ids": [ "acquired-protocol-c7f45d872952b996c96a" ], "state": "charts_available", "source_ids": [ "acquired-source-3156602fda847ae943b4" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM13_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-f6bf921e477601ffffec", "kind": "protocol", "name": "BEELINE 2020 Figure 4 · mCAD · {}", "status": "discovered", "url": "/database/protocol/acquired-protocol-f6bf921e477601ffffec/", "evaluations": 12, "metric_rows": 48, "charts": 4, "charted_metric_rows": 48, "chart_protocol_ids": [ "acquired-protocol-f6bf921e477601ffffec" ], "state": "charts_available", "source_ids": [ "acquired-source-3156602fda847ae943b4" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM13_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-37b5599b7d976211e8c1", "kind": "protocol", "name": "BEELINE 2020 Figure 4 · VSC · {}", "status": "discovered", "url": "/database/protocol/acquired-protocol-37b5599b7d976211e8c1/", "evaluations": 12, "metric_rows": 36, "charts": 3, "charted_metric_rows": 36, "chart_protocol_ids": [ "acquired-protocol-37b5599b7d976211e8c1" ], "state": "charts_available", "source_ids": [ "acquired-source-3156602fda847ae943b4" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM13_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-30ca92be5250d3347718", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · hESC · {\"reference_network\":\"Cell-type specific ChIP-Seq\",\"gene_selection\":\"TFs+1000\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-30ca92be5250d3347718/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-30ca92be5250d3347718" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-a930238c7acc35fd34ee", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · hESC · {\"reference_network\":\"Cell-type specific ChIP-Seq\",\"gene_selection\":\"TFs+500\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-a930238c7acc35fd34ee/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-a930238c7acc35fd34ee" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-bd9b01304308808a7b38", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · hESC · {\"reference_network\":\"Non-specific ChIP-Seq\",\"gene_selection\":\"TFs+1000\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-bd9b01304308808a7b38/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-bd9b01304308808a7b38" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-eceec78306355eece4e7", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · hESC · {\"reference_network\":\"Non-specific ChIP-Seq\",\"gene_selection\":\"TFs+500\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-eceec78306355eece4e7/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-eceec78306355eece4e7" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-b3a78798ab8a7602a63a", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · hESC · {\"reference_network\":\"STRING\",\"gene_selection\":\"TFs+1000\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-b3a78798ab8a7602a63a/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-b3a78798ab8a7602a63a" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-6ddc5a89a2b4c4c474d7", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · hESC · {\"reference_network\":\"STRING\",\"gene_selection\":\"TFs+500\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-6ddc5a89a2b4c4c474d7/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-6ddc5a89a2b4c4c474d7" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-4178cb595371e239c8fd", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · hHep · {\"reference_network\":\"Cell-type specific ChIP-Seq\",\"gene_selection\":\"TFs+1000\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-4178cb595371e239c8fd/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-4178cb595371e239c8fd" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-34109c3e92506dce8489", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · hHep · {\"reference_network\":\"Cell-type specific ChIP-Seq\",\"gene_selection\":\"TFs+500\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-34109c3e92506dce8489/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-34109c3e92506dce8489" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-e0ffaca06ad1222ac21e", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · hHep · {\"reference_network\":\"Non-specific ChIP-Seq\",\"gene_selection\":\"TFs+1000\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-e0ffaca06ad1222ac21e/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-e0ffaca06ad1222ac21e" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-81fdcee5288c3672584a", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · hHep · {\"reference_network\":\"Non-specific ChIP-Seq\",\"gene_selection\":\"TFs+500\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-81fdcee5288c3672584a/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-81fdcee5288c3672584a" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-2a8b0faaeabb2b42f8fb", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · hHep · {\"reference_network\":\"STRING\",\"gene_selection\":\"TFs+1000\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-2a8b0faaeabb2b42f8fb/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-2a8b0faaeabb2b42f8fb" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-994c136cc78955a7777e", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · hHep · {\"reference_network\":\"STRING\",\"gene_selection\":\"TFs+500\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-994c136cc78955a7777e/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-994c136cc78955a7777e" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-b782c1901e3d8fb8348e", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · mDC · {\"reference_network\":\"Cell-type specific ChIP-Seq\",\"gene_selection\":\"TFs+1000\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-b782c1901e3d8fb8348e/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-b782c1901e3d8fb8348e" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-4745597f348c3ff0e85a", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · mDC · {\"reference_network\":\"Cell-type specific ChIP-Seq\",\"gene_selection\":\"TFs+500\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-4745597f348c3ff0e85a/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-4745597f348c3ff0e85a" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-1227fd691dca8a3aa41d", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · mDC · {\"reference_network\":\"Non-specific ChIP-Seq\",\"gene_selection\":\"TFs+1000\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-1227fd691dca8a3aa41d/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-1227fd691dca8a3aa41d" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-3c4df1f88f28c01a7508", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · mDC · {\"reference_network\":\"Non-specific ChIP-Seq\",\"gene_selection\":\"TFs+500\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-3c4df1f88f28c01a7508/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-3c4df1f88f28c01a7508" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-a72274bbb664040489be", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · mDC · {\"reference_network\":\"STRING\",\"gene_selection\":\"TFs+1000\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-a72274bbb664040489be/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-a72274bbb664040489be" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-edb7d264956f89df17fc", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · mDC · {\"reference_network\":\"STRING\",\"gene_selection\":\"TFs+500\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-edb7d264956f89df17fc/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-edb7d264956f89df17fc" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-7f7b37c767904dd8a6fb", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · mESC · {\"reference_network\":\"Cell-type specific ChIP-Seq\",\"gene_selection\":\"TFs+1000\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-7f7b37c767904dd8a6fb/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-7f7b37c767904dd8a6fb" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-024f47659eb7e75f56dc", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · mESC · {\"reference_network\":\"Cell-type specific ChIP-Seq\",\"gene_selection\":\"TFs+500\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-024f47659eb7e75f56dc/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-024f47659eb7e75f56dc" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-b1b289fa63273aa8bba2", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · mESC · {\"reference_network\":\"log/gof\",\"gene_selection\":\"TFs+1000\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-b1b289fa63273aa8bba2/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-b1b289fa63273aa8bba2" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-174f1a5acdc3c13db7b2", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · mESC · {\"reference_network\":\"log/gof\",\"gene_selection\":\"TFs+500\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-174f1a5acdc3c13db7b2/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-174f1a5acdc3c13db7b2" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-fbb04bf73e09481732c8", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · mESC · {\"reference_network\":\"Non-specific ChIP-Seq\",\"gene_selection\":\"TFs+1000\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-fbb04bf73e09481732c8/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-fbb04bf73e09481732c8" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-dc2ce864a7578927cabc", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · mESC · {\"reference_network\":\"Non-specific ChIP-Seq\",\"gene_selection\":\"TFs+500\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-dc2ce864a7578927cabc/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-dc2ce864a7578927cabc" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-b7da29c68a46720cce0b", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · mESC · {\"reference_network\":\"STRING\",\"gene_selection\":\"TFs+1000\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-b7da29c68a46720cce0b/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-b7da29c68a46720cce0b" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-7913b13aba9d987c38ae", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · mESC · {\"reference_network\":\"STRING\",\"gene_selection\":\"TFs+500\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-7913b13aba9d987c38ae/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-7913b13aba9d987c38ae" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-b614e3405917763fb159", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · mHSC-E · {\"reference_network\":\"Cell-type specific ChIP-Seq\",\"gene_selection\":\"TFs+1000\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-b614e3405917763fb159/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-b614e3405917763fb159" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-b022aafcf374cd51f0f3", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · mHSC-E · {\"reference_network\":\"Cell-type specific ChIP-Seq\",\"gene_selection\":\"TFs+500\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-b022aafcf374cd51f0f3/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-b022aafcf374cd51f0f3" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-f4f5a4cb785dc55503bb", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · mHSC-E · {\"reference_network\":\"Non-specific ChIP-Seq\",\"gene_selection\":\"TFs+1000\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-f4f5a4cb785dc55503bb/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-f4f5a4cb785dc55503bb" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-51354be75f1492ed099a", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · mHSC-E · {\"reference_network\":\"Non-specific ChIP-Seq\",\"gene_selection\":\"TFs+500\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-51354be75f1492ed099a/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-51354be75f1492ed099a" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-a9a52bfc61cc00ae40eb", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · mHSC-E · {\"reference_network\":\"STRING\",\"gene_selection\":\"TFs+1000\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-a9a52bfc61cc00ae40eb/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-a9a52bfc61cc00ae40eb" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-78f8093a50e8fca5eacc", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · mHSC-E · {\"reference_network\":\"STRING\",\"gene_selection\":\"TFs+500\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-78f8093a50e8fca5eacc/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-78f8093a50e8fca5eacc" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-408cb9c598ef659f51a6", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · MHSC-GM · {\"reference_network\":\"Cell-type specific ChIP-Seq\",\"gene_selection\":\"TFs+1000\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-408cb9c598ef659f51a6/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-408cb9c598ef659f51a6" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-f6bd2f323f0f81692075", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · MHSC-GM · {\"reference_network\":\"Cell-type specific ChIP-Seq\",\"gene_selection\":\"TFs+500\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-f6bd2f323f0f81692075/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-f6bd2f323f0f81692075" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-a8f87266d6be53bbd23b", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · MHSC-GM · {\"reference_network\":\"Non-specific ChIP-Seq\",\"gene_selection\":\"TFs+1000\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-a8f87266d6be53bbd23b/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-a8f87266d6be53bbd23b" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-ceaaa7b9d8af61e51736", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · MHSC-GM · {\"reference_network\":\"Non-specific ChIP-Seq\",\"gene_selection\":\"TFs+500\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-ceaaa7b9d8af61e51736/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-ceaaa7b9d8af61e51736" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-c8cff8ffd3fbf524bf2e", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · MHSC-GM · {\"reference_network\":\"STRING\",\"gene_selection\":\"TFs+1000\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-c8cff8ffd3fbf524bf2e/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-c8cff8ffd3fbf524bf2e" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-c57e646de930422fa536", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · MHSC-GM · {\"reference_network\":\"STRING\",\"gene_selection\":\"TFs+500\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-c57e646de930422fa536/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-c57e646de930422fa536" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-d60261afa2c58e4aa12e", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · mHSC-L · {\"reference_network\":\"Cell-type specific ChIP-Seq\",\"gene_selection\":\"TFs+1000\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-d60261afa2c58e4aa12e/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-d60261afa2c58e4aa12e" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-f7ef0c77a6155a1ff0d4", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · mHSC-L · {\"reference_network\":\"Cell-type specific ChIP-Seq\",\"gene_selection\":\"TFs+500\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-f7ef0c77a6155a1ff0d4/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-f7ef0c77a6155a1ff0d4" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-bd571aa3305cceba1f0b", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · mHSC-L · {\"reference_network\":\"Non-specific ChIP-Seq\",\"gene_selection\":\"TFs+1000\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-bd571aa3305cceba1f0b/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-bd571aa3305cceba1f0b" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-ed61833eb749ba711c5b", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · mHSC-L · {\"reference_network\":\"Non-specific ChIP-Seq\",\"gene_selection\":\"TFs+500\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-ed61833eb749ba711c5b/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-ed61833eb749ba711c5b" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-7977f5aa02ec0001bc1a", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · mHSC-L · {\"reference_network\":\"STRING\",\"gene_selection\":\"TFs+1000\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-7977f5aa02ec0001bc1a/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-7977f5aa02ec0001bc1a" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-61ae01473c4e5c4a9ce5", "kind": "protocol", "name": "BEELINE 2020 Figure 5 · mHSC-L · {\"reference_network\":\"STRING\",\"gene_selection\":\"TFs+500\"}", "status": "discovered", "url": "/database/protocol/acquired-protocol-61ae01473c4e5c4a9ce5/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "acquired-protocol-61ae01473c4e5c4a9ce5" ], "state": "charts_available", "source_ids": [ "acquired-source-31344fb7e5e8ae6b9666" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41592-019-0690-6/MediaObjects/41592_2019_690_MOESM14_ESM.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "paper-protocol-208a8085432aa64eb2", "kind": "protocol", "name": "bpRNA-TS0 (RNA secondary structure)", "status": "needs_review", "url": "/database/protocol/paper-protocol-208a8085432aa64eb2/", "evaluations": 10, "metric_rows": 40, "charts": 4, "charted_metric_rows": 40, "chart_protocol_ids": [ "paper-protocol-208a8085432aa64eb2" ], "state": "charts_available", "source_ids": [ "bpfold-2025" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12216785/" ], "research_status": "complete_tables_extracted", "research_review_date": "2026-09-17", "gaps": [ "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "uc-clinical-20260930-enigma-brca1-protocol", "kind": "protocol", "name": "BRCA1 BayesDel evidence calibration", "status": "source_checked", "url": "/database/protocol/uc-clinical-20260930-enigma-brca1-protocol/", "evaluations": 1, "metric_rows": 15, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "uc-clinical-20260930-source-enigma" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC11393667/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "uc-clinical-20260930-enigma-brca1-generic-protocol", "kind": "protocol", "name": "BRCA1 generic BayesDel threshold evidence-code assignment", "status": "source_checked", "url": "/database/protocol/uc-clinical-20260930-enigma-brca1-generic-protocol/", "evaluations": 1, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "uc-clinical-20260930-source-enigma" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC11393667/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "uc-clinical-20260930-enigma-brca2-protocol", "kind": "protocol", "name": "BRCA2 BayesDel evidence calibration", "status": "source_checked", "url": "/database/protocol/uc-clinical-20260930-enigma-brca2-protocol/", "evaluations": 1, "metric_rows": 15, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "uc-clinical-20260930-source-enigma" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC11393667/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "uc-clinical-20260930-enigma-brca2-generic-protocol", "kind": "protocol", "name": "BRCA2 generic BayesDel threshold evidence-code assignment", "status": "source_checked", "url": "/database/protocol/uc-clinical-20260930-enigma-brca2-generic-protocol/", "evaluations": 1, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "uc-clinical-20260930-source-enigma" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC11393667/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-906c90560bda45e6b1af", "kind": "protocol", "name": "CAFA3 BPO all organisms; type1 no-knowledge; mode1 · CAFA3 final benchmark; BPO; all; type1; mode1", "status": "discovered", "url": "/database/protocol/acquired-protocol-906c90560bda45e6b1af/", "evaluations": 146, "metric_rows": 146, "charts": 2, "charted_metric_rows": 146, "chart_protocol_ids": [ "acquired-protocol-906c90560bda45e6b1af" ], "state": "charts_available", "source_ids": [ "acquired-source-8729ad22565c7a738b41" ], "source_urls": [ "https://ndownloader.figshare.com/files/17519846" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-a8ac152e52ee3e06387c", "kind": "protocol", "name": "CAFA3 CCO all organisms; type1 no-knowledge; mode1 · CAFA3 final benchmark; CCO; all; type1; mode1", "status": "discovered", "url": "/database/protocol/acquired-protocol-a8ac152e52ee3e06387c/", "evaluations": 146, "metric_rows": 146, "charts": 2, "charted_metric_rows": 146, "chart_protocol_ids": [ "acquired-protocol-a8ac152e52ee3e06387c" ], "state": "charts_available", "source_ids": [ "acquired-source-8594fdd08941d9338591" ], "source_urls": [ "https://ndownloader.figshare.com/files/17519846" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-0841c618c0a89fa56f63", "kind": "protocol", "name": "CAFA3 MFO all organisms; type1 no-knowledge; mode1 · CAFA3 final benchmark; MFO; all; type1; mode1", "status": "discovered", "url": "/database/protocol/acquired-protocol-0841c618c0a89fa56f63/", "evaluations": 146, "metric_rows": 146, "charts": 2, "charted_metric_rows": 146, "chart_protocol_ids": [ "acquired-protocol-0841c618c0a89fa56f63" ], "state": "charts_available", "source_ids": [ "acquired-source-7470044466b466152cf1" ], "source_urls": [ "https://ndownloader.figshare.com/files/17519846" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "alphagenome-2026-t3-protocol-11", "kind": "protocol", "name": "CAGE track prediction at 128 bp (AlphaGenome paper)", "status": "needs_review", "url": "/database/protocol/alphagenome-2026-t3-protocol-11/", "evaluations": 3, "metric_rows": 3, "charts": 1, "charted_metric_rows": 3, "chart_protocol_ids": [ "alphagenome-2026-t3-protocol-11" ], "state": "charts_available", "source_ids": [ "source-alphagenome-nature2026-tables", "source-alphagenome-nature2026-supplementary-methods", "evidence-official-56e5abfb5f12f1cd3b20" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-025-10014-0/MediaObjects/41586_2025_10014_MOESM3_ESM.xlsx", "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-025-10014-0/MediaObjects/41586_2025_10014_MOESM1_ESM.pdf", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12851941/" ], "research_status": "complete_comparison_extracted", "research_review_date": "2026-09-17", "gaps": [ "Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked.", "Subsequent studies use different datasets and are not pooled with this paper." ] }, { "id": "alphagenome-2026-t3-protocol-10", "kind": "protocol", "name": "CAGE track prediction at 32 bp (AlphaGenome paper)", "status": "needs_review", "url": "/database/protocol/alphagenome-2026-t3-protocol-10/", "evaluations": 2, "metric_rows": 2, "charts": 1, "charted_metric_rows": 2, "chart_protocol_ids": [ "alphagenome-2026-t3-protocol-10" ], "state": "charts_available", "source_ids": [ "source-alphagenome-nature2026-tables", "source-alphagenome-nature2026-supplementary-methods", "evidence-official-56e5abfb5f12f1cd3b20" ], "source_urls": [ "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-025-10014-0/MediaObjects/41586_2025_10014_MOESM3_ESM.xlsx", "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-025-10014-0/MediaObjects/41586_2025_10014_MOESM1_ESM.pdf", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12851941/" ], "research_status": "complete_comparison_extracted", "research_review_date": "2026-09-17", "gaps": [ "Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked.", "Subsequent studies use different datasets and are not pooled with this paper." ] }, { "id": "acquired-protocol-f443b5fdaee9129f2b7a", "kind": "protocol", "name": "CAMI II marine genome binning; pooled short-read gold-standard assembly; circular elements excluded · marmgCAMI2_short_read_pooled_gold_standard_assembly", "status": "discovered", "url": "/database/protocol/acquired-protocol-f443b5fdaee9129f2b7a/", "evaluations": 16, "metric_rows": 256, "charts": 16, "charted_metric_rows": 256, "chart_protocol_ids": [ "acquired-protocol-f443b5fdaee9129f2b7a" ], "state": "charts_available", "source_ids": [ "acquired-source-f64302952624afe35a58" ], "source_urls": [ "https://raw.githubusercontent.com/CAMI-challenge/second_challenge_evaluation/501b543f65d62e5c1d6c3813be0badcac5e079ca/binning/genome_binning/marine_dataset/results/amber_marine_nocircular/results.tsv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-287b8fe8904985b6e420", "kind": "protocol", "name": "CAPRI round 61 predictor; submitted model 1; T312.1 · CAPRI round 61 T312.1", "status": "discovered", "url": "/database/protocol/acquired-protocol-287b8fe8904985b6e420/", "evaluations": 25, "metric_rows": 100, "charts": 4, "charted_metric_rows": 100, "chart_protocol_ids": [ "acquired-protocol-287b8fe8904985b6e420" ], "state": "charts_available", "source_ids": [ "acquired-source-a1e1af10cf13322916ca" ], "source_urls": [ "https://www.capri-docking.org/assessment/files/round61.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-95bb2d71a1d51316f506", "kind": "protocol", "name": "CAPRI round 61 predictor; submitted model 1; T314.1 · CAPRI round 61 T314.1", "status": "discovered", "url": "/database/protocol/acquired-protocol-95bb2d71a1d51316f506/", "evaluations": 25, "metric_rows": 100, "charts": 4, "charted_metric_rows": 100, "chart_protocol_ids": [ "acquired-protocol-95bb2d71a1d51316f506" ], "state": "charts_available", "source_ids": [ "acquired-source-a1e1af10cf13322916ca" ], "source_urls": [ "https://www.capri-docking.org/assessment/files/round61.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-e7121a74a668c30652c8", "kind": "protocol", "name": "CAPRI round 61 predictor; submitted model 1; T315.1 · CAPRI round 61 T315.1", "status": "discovered", "url": "/database/protocol/acquired-protocol-e7121a74a668c30652c8/", "evaluations": 25, "metric_rows": 100, "charts": 4, "charted_metric_rows": 100, "chart_protocol_ids": [ "acquired-protocol-e7121a74a668c30652c8" ], "state": "charts_available", "source_ids": [ "acquired-source-a1e1af10cf13322916ca" ], "source_urls": [ "https://www.capri-docking.org/assessment/files/round61.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-cedd42f89ef2860a1fc7", "kind": "protocol", "name": "CAPRI round 61 predictor; submitted model 1; T316.1 · CAPRI round 61 T316.1", "status": "discovered", "url": "/database/protocol/acquired-protocol-cedd42f89ef2860a1fc7/", "evaluations": 25, "metric_rows": 100, "charts": 4, "charted_metric_rows": 100, "chart_protocol_ids": [ "acquired-protocol-cedd42f89ef2860a1fc7" ], "state": "charts_available", "source_ids": [ "acquired-source-a1e1af10cf13322916ca" ], "source_urls": [ "https://www.capri-docking.org/assessment/files/round61.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "paper-protocol-9e3344661a0f282e5e", "kind": "protocol", "name": "CASF-2016 docking (Protein–ligand binding affinity scoring)", "status": "needs_review", "url": "/database/protocol/paper-protocol-9e3344661a0f282e5e/", "evaluations": 9, "metric_rows": 27, "charts": 3, "charted_metric_rows": 27, "chart_protocol_ids": [ "paper-protocol-9e3344661a0f282e5e" ], "state": "charts_available", "source_ids": [ "akscore-2020" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC7697539/" ], "research_status": "complete_tables_extracted", "research_review_date": "2026-09-17", "gaps": [ "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "paper-protocol-0c5a1c5ef6896a2d96", "kind": "protocol", "name": "CASF-2016 ranking (Protein–ligand binding affinity scoring)", "status": "needs_review", "url": "/database/protocol/paper-protocol-0c5a1c5ef6896a2d96/", "evaluations": 9, "metric_rows": 27, "charts": 3, "charted_metric_rows": 27, "chart_protocol_ids": [ "paper-protocol-0c5a1c5ef6896a2d96" ], "state": "charts_available", "source_ids": [ "akscore-2020" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC7697539/" ], "research_status": "complete_tables_extracted", "research_review_date": "2026-09-17", "gaps": [ "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "paper-protocol-31d4bca49fb09d2e6f", "kind": "protocol", "name": "CASF-2016 scoring (Protein–ligand binding affinity scoring)", "status": "needs_review", "url": "/database/protocol/paper-protocol-31d4bca49fb09d2e6f/", "evaluations": 9, "metric_rows": 9, "charts": 1, "charted_metric_rows": 9, "chart_protocol_ids": [ "paper-protocol-31d4bca49fb09d2e6f" ], "state": "charts_available", "source_ids": [ "akscore-2020" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC7697539/" ], "research_status": "complete_tables_extracted", "research_review_date": "2026-09-17", "gaps": [ "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "acquired-protocol-8068932c1a23c9c3f049", "kind": "protocol", "name": "CASP16 protein domain; first submitted model; T1201-D1 · CASP16 T1201-D1", "status": "discovered", "url": "/database/protocol/acquired-protocol-8068932c1a23c9c3f049/", "evaluations": 90, "metric_rows": 270, "charts": 6, "charted_metric_rows": 270, "chart_protocol_ids": [ "acquired-protocol-8068932c1a23c9c3f049" ], "state": "charts_available", "source_ids": [ "acquired-source-9156fdf9eed96dcdafaa" ], "source_urls": [ "https://predictioncenter.org/download_area/CASP16/results/tables/CASP16_prot_domains.scores.csv" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. 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Individual observations remain in the results table." ] }, { "id": "paper-protocol-bbffa94da73852557b", "kind": "protocol", "name": "Clathrin independent test: selected-embedding classifiers (clathrin protein classification)", "status": "needs_review", "url": "/database/protocol/paper-protocol-bbffa94da73852557b/", "evaluations": 13, "metric_rows": 78, "charts": 6, "charted_metric_rows": 78, "chart_protocol_ids": [ "paper-protocol-bbffa94da73852557b" ], "state": "charts_available", "source_ids": [ "part2-clathrin-plm-2025" ], "source_urls": [ "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12238356/fullTextXML" ], "research_status": "complete_comparison_tables_extracted_pending_publication_review", "research_review_date": "2026-09-17", "gaps": [ "Independent batch review before import; preserve existing observation identities." ] }, { "id": "ucc-docking-cluspro-bm5-2020-protocol-bound-antibody-top10", "kind": "protocol", "name": "ClusPro BM5 Bound antibody top10", "status": "source_checked", "url": "/database/protocol/ucc-docking-cluspro-bm5-2020-protocol-bound-antibody-top10/", "evaluations": 1, "metric_rows": 9, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "ucc-docking-cluspro-bm5-2020-source" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC7484347/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "ucc-docking-cluspro-bm5-2020-protocol-bound-antibody-top30", "kind": "protocol", "name": "ClusPro BM5 Bound antibody top30", "status": "source_checked", "url": "/database/protocol/ucc-docking-cluspro-bm5-2020-protocol-bound-antibody-top30/", "evaluations": 1, "metric_rows": 9, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "ucc-docking-cluspro-bm5-2020-source" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC7484347/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "ucc-docking-cluspro-bm5-2020-protocol-total-difficult-top10", "kind": "protocol", "name": "ClusPro BM5 difficult aggregate top10", "status": "source_checked", "url": "/database/protocol/ucc-docking-cluspro-bm5-2020-protocol-total-difficult-top10/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "ucc-docking-cluspro-bm5-2020-source" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC7484347/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "ucc-docking-cluspro-bm5-2020-protocol-total-difficult-top30", "kind": "protocol", "name": "ClusPro BM5 difficult aggregate top30", "status": "source_checked", "url": "/database/protocol/ucc-docking-cluspro-bm5-2020-protocol-total-difficult-top30/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "ucc-docking-cluspro-bm5-2020-source" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC7484347/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "ucc-docking-cluspro-bm5-2020-protocol-total-easy-top10", "kind": "protocol", "name": "ClusPro BM5 easy aggregate top10", "status": "source_checked", "url": "/database/protocol/ucc-docking-cluspro-bm5-2020-protocol-total-easy-top10/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "ucc-docking-cluspro-bm5-2020-source" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC7484347/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "ucc-docking-cluspro-bm5-2020-protocol-total-easy-top30", "kind": "protocol", "name": "ClusPro BM5 easy aggregate top30", "status": "source_checked", "url": "/database/protocol/ucc-docking-cluspro-bm5-2020-protocol-total-easy-top30/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "ucc-docking-cluspro-bm5-2020-source" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC7484347/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "ucc-docking-cluspro-bm5-2020-protocol-enzyme-top10", "kind": "protocol", "name": "ClusPro BM5 Enzyme top10", "status": "source_checked", "url": "/database/protocol/ucc-docking-cluspro-bm5-2020-protocol-enzyme-top10/", "evaluations": 1, "metric_rows": 11, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "ucc-docking-cluspro-bm5-2020-source" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC7484347/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "ucc-docking-cluspro-bm5-2020-protocol-enzyme-top30", "kind": "protocol", "name": "ClusPro BM5 Enzyme top30", "status": "source_checked", "url": "/database/protocol/ucc-docking-cluspro-bm5-2020-protocol-enzyme-top30/", "evaluations": 1, "metric_rows": 11, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "ucc-docking-cluspro-bm5-2020-source" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC7484347/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "ucc-docking-cluspro-bm5-2020-protocol-total-intermediate-top10", "kind": "protocol", "name": "ClusPro BM5 intermediate aggregate top10", "status": "source_checked", "url": "/database/protocol/ucc-docking-cluspro-bm5-2020-protocol-total-intermediate-top10/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "ucc-docking-cluspro-bm5-2020-source" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC7484347/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "ucc-docking-cluspro-bm5-2020-protocol-total-intermediate-top30", "kind": "protocol", "name": "ClusPro BM5 intermediate aggregate top30", "status": "source_checked", "url": "/database/protocol/ucc-docking-cluspro-bm5-2020-protocol-total-intermediate-top30/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "ucc-docking-cluspro-bm5-2020-source" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC7484347/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "ucc-docking-cluspro-bm5-2020-protocol-others-top10", "kind": "protocol", "name": "ClusPro BM5 Others top10", "status": "source_checked", "url": "/database/protocol/ucc-docking-cluspro-bm5-2020-protocol-others-top10/", "evaluations": 1, "metric_rows": 11, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "ucc-docking-cluspro-bm5-2020-source" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC7484347/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "ucc-docking-cluspro-bm5-2020-protocol-others-top30", "kind": "protocol", "name": "ClusPro BM5 Others top30", "status": "source_checked", "url": "/database/protocol/ucc-docking-cluspro-bm5-2020-protocol-others-top30/", "evaluations": 1, "metric_rows": 11, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "ucc-docking-cluspro-bm5-2020-source" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC7484347/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "ucc-docking-cluspro-bm5-2020-protocol-total-top10", "kind": "protocol", "name": "ClusPro BM5 Total top10", "status": "source_checked", "url": "/database/protocol/ucc-docking-cluspro-bm5-2020-protocol-total-top10/", "evaluations": 1, "metric_rows": 10, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "ucc-docking-cluspro-bm5-2020-source" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC7484347/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "ucc-docking-cluspro-bm5-2020-protocol-total-top30", "kind": "protocol", "name": "ClusPro BM5 Total top30", "status": "source_checked", "url": "/database/protocol/ucc-docking-cluspro-bm5-2020-protocol-total-top30/", "evaluations": 1, "metric_rows": 11, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "ucc-docking-cluspro-bm5-2020-source" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC7484347/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. 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Individual observations remain in the results table." ] }, { "id": "acquired-protocol-5e6866875f05d71b27d6", "kind": "protocol", "name": "FLIP2 Amylase by-mutation; held-out test set · Amylase", "status": "discovered", "url": "/database/protocol/acquired-protocol-5e6866875f05d71b27d6/", "evaluations": 9, "metric_rows": 18, "charts": 2, "charted_metric_rows": 18, "chart_protocol_ids": [ "acquired-protocol-5e6866875f05d71b27d6" ], "state": "charts_available", "source_ids": [ "evidence-expansion-flip2-d0e61ca2" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_manuscipt.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-677b87f02518f844ef73", "kind": "protocol", "name": "FLIP2 Amylase close-to-far; held-out test set · Amylase", "status": "discovered", "url": "/database/protocol/acquired-protocol-677b87f02518f844ef73/", "evaluations": 9, "metric_rows": 17, "charts": 2, "charted_metric_rows": 17, "chart_protocol_ids": [ "acquired-protocol-677b87f02518f844ef73" ], "state": "charts_available", "source_ids": [ "evidence-expansion-flip2-d0e61ca2" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_manuscipt.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-467d2c2551a1f523408b", "kind": "protocol", "name": "FLIP2 Amylase far-to-close; held-out test set · Amylase", "status": "discovered", "url": "/database/protocol/acquired-protocol-467d2c2551a1f523408b/", "evaluations": 9, "metric_rows": 18, "charts": 2, "charted_metric_rows": 18, "chart_protocol_ids": [ "acquired-protocol-467d2c2551a1f523408b" ], "state": "charts_available", "source_ids": [ "evidence-expansion-flip2-d0e61ca2" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_manuscipt.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-86d9b432edaa8d609e23", "kind": "protocol", "name": "FLIP2 Amylase one-to-many; held-out test set · Amylase", "status": "discovered", "url": "/database/protocol/acquired-protocol-86d9b432edaa8d609e23/", "evaluations": 9, "metric_rows": 18, "charts": 2, "charted_metric_rows": 18, "chart_protocol_ids": [ "acquired-protocol-86d9b432edaa8d609e23" ], "state": "charts_available", "source_ids": [ "evidence-expansion-flip2-d0e61ca2" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_manuscipt.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-2a25c278d301f1b27a06", "kind": "protocol", "name": "FLIP2 hydro low-to-high; held-out test set · hydro", "status": "discovered", "url": "/database/protocol/acquired-protocol-2a25c278d301f1b27a06/", "evaluations": 9, "metric_rows": 18, "charts": 2, "charted_metric_rows": 18, "chart_protocol_ids": [ "acquired-protocol-2a25c278d301f1b27a06" ], "state": "charts_available", "source_ids": [ "evidence-expansion-flip2-d0e61ca2" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_manuscipt.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-56154db2cb24cf00a2e4", "kind": "protocol", "name": "FLIP2 hydro three-to-many; held-out test set · hydro", "status": "discovered", "url": "/database/protocol/acquired-protocol-56154db2cb24cf00a2e4/", "evaluations": 9, "metric_rows": 18, "charts": 2, "charted_metric_rows": 18, "chart_protocol_ids": [ "acquired-protocol-56154db2cb24cf00a2e4" ], "state": "charts_available", "source_ids": [ "evidence-expansion-flip2-d0e61ca2" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_manuscipt.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-07f31785d85b3d526033", "kind": "protocol", "name": "FLIP2 hydro to-P01053; held-out test set · hydro", "status": "discovered", "url": "/database/protocol/acquired-protocol-07f31785d85b3d526033/", "evaluations": 9, "metric_rows": 17, "charts": 2, "charted_metric_rows": 17, "chart_protocol_ids": [ "acquired-protocol-07f31785d85b3d526033" ], "state": "charts_available", "source_ids": [ "evidence-expansion-flip2-d0e61ca2" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_manuscipt.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-8d1a268f98d747f4c385", "kind": "protocol", "name": "FLIP2 hydro to-P06241; held-out test set · hydro", "status": "discovered", "url": "/database/protocol/acquired-protocol-8d1a268f98d747f4c385/", "evaluations": 9, "metric_rows": 18, "charts": 2, "charted_metric_rows": 18, "chart_protocol_ids": [ "acquired-protocol-8d1a268f98d747f4c385" ], "state": "charts_available", "source_ids": [ "evidence-expansion-flip2-d0e61ca2" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_manuscipt.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-e693882416f4067e6939", "kind": "protocol", "name": "FLIP2 hydro to-P0A9X9; held-out test set · hydro", "status": "discovered", "url": "/database/protocol/acquired-protocol-e693882416f4067e6939/", "evaluations": 9, "metric_rows": 18, "charts": 2, "charted_metric_rows": 18, "chart_protocol_ids": [ "acquired-protocol-e693882416f4067e6939" ], "state": "charts_available", "source_ids": [ "evidence-expansion-flip2-d0e61ca2" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_manuscipt.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-d0d5f30d1e07aa33d121", "kind": "protocol", "name": "FLIP2 IRED two-to-many; held-out test set · IRED", "status": "discovered", "url": "/database/protocol/acquired-protocol-d0d5f30d1e07aa33d121/", "evaluations": 9, "metric_rows": 18, "charts": 2, "charted_metric_rows": 18, "chart_protocol_ids": [ "acquired-protocol-d0d5f30d1e07aa33d121" ], "state": "charts_available", "source_ids": [ "evidence-expansion-flip2-d0e61ca2" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_manuscipt.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-06a6cc45005b6e951779", "kind": "protocol", "name": "FLIP2 NucB two-to-many; held-out test set · NucB", "status": "discovered", "url": "/database/protocol/acquired-protocol-06a6cc45005b6e951779/", "evaluations": 9, "metric_rows": 18, "charts": 2, "charted_metric_rows": 18, "chart_protocol_ids": [ "acquired-protocol-06a6cc45005b6e951779" ], "state": "charts_available", "source_ids": [ "evidence-expansion-flip2-d0e61ca2" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_manuscipt.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-c28293280f628951a96d", "kind": "protocol", "name": "FLIP2 PDZ3 single-to-double; held-out test set · PDZ3", "status": "discovered", "url": "/database/protocol/acquired-protocol-c28293280f628951a96d/", "evaluations": 9, "metric_rows": 17, "charts": 2, "charted_metric_rows": 17, "chart_protocol_ids": [ "acquired-protocol-c28293280f628951a96d" ], "state": "charts_available", "source_ids": [ "evidence-expansion-flip2-d0e61ca2" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_manuscipt.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "rewire-protocol-flip2-rhomax-by-wild-type-v1", "kind": "protocol", "name": "FLIP2 Rhomax by_wild_type", "status": "source_checked", "url": "/database/protocol/rewire-protocol-flip2-rhomax-by-wild-type-v1/", "evaluations": 5, "metric_rows": 10, "charts": 1, "charted_metric_rows": 2, "chart_protocol_ids": [ "rewire-protocol-flip2-rhomax-by-wild-type-v1" ], "state": "charts_available", "source_ids": [ "rewire-local-20260920-source-flip2-composition", "rewire-local-20260920-instructions-flip2" ], "source_urls": [ "https://github.com/rewire-bio/rewire-benchmarks/blob/ca73fa47136d182f2d4ddb083d084712198fc0e2/research/local-runs-2026-09-20/flip2-composition/report.json", "https://github.com/rewire-bio/rewire-benchmarks/blob/ca73fa47136d182f2d4ddb083d084712198fc0e2/research/local-runs-2026-09-20/README.md" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-d689343c656902d1f852", "kind": "protocol", "name": "FLIP2 rhomax by-wild-type; held-out test set · rhomax", "status": "discovered", "url": "/database/protocol/acquired-protocol-d689343c656902d1f852/", "evaluations": 9, "metric_rows": 17, "charts": 2, "charted_metric_rows": 17, "chart_protocol_ids": [ "acquired-protocol-d689343c656902d1f852" ], "state": "charts_available", "source_ids": [ "evidence-expansion-flip2-d0e61ca2" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_manuscipt.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-ed315b25923fa3e1f9a6", "kind": "protocol", "name": "FLIP2 TrpB by-position; held-out test set · TrpB", "status": "discovered", "url": "/database/protocol/acquired-protocol-ed315b25923fa3e1f9a6/", "evaluations": 9, "metric_rows": 18, "charts": 2, "charted_metric_rows": 18, "chart_protocol_ids": [ "acquired-protocol-ed315b25923fa3e1f9a6" ], "state": "charts_available", "source_ids": [ "evidence-expansion-flip2-d0e61ca2" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_manuscipt.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-40d273a00b4110007da3", "kind": "protocol", "name": "FLIP2 TrpB one-to-many; held-out test set · TrpB", "status": "discovered", "url": "/database/protocol/acquired-protocol-40d273a00b4110007da3/", "evaluations": 9, "metric_rows": 17, "charts": 2, "charted_metric_rows": 17, "chart_protocol_ids": [ "acquired-protocol-40d273a00b4110007da3" ], "state": "charts_available", "source_ids": [ "evidence-expansion-flip2-d0e61ca2" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_manuscipt.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "acquired-protocol-4c2b9e709bc390708ebd", "kind": "protocol", "name": "FLIP2 TrpB two-to-many; held-out test set · TrpB", "status": "discovered", "url": "/database/protocol/acquired-protocol-4c2b9e709bc390708ebd/", "evaluations": 9, "metric_rows": 18, "charts": 2, "charted_metric_rows": 18, "chart_protocol_ids": [ "acquired-protocol-4c2b9e709bc390708ebd" ], "state": "charts_available", "source_ids": [ "evidence-expansion-flip2-d0e61ca2" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_manuscipt.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "ucc-research-protocol-foldbench-antibody-antigen", "kind": "protocol", "name": "FoldBench antibody-antigen published full-set assessment", "status": "source_checked", "url": "/database/protocol/ucc-research-protocol-foldbench-antibody-antigen/", "evaluations": 5, "metric_rows": 20, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "ucc-research-source-foldbench-paper", "ucc-research-source-foldbench-supp", "ucc-research-source-foldbench-code" ], "source_urls": [ "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12800276/fullTextXML", "https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-025-67127-3/MediaObjects/41467_2025_67127_MOESM1_ESM.pdf", "https://raw.githubusercontent.com/BEAM-Labs/FoldBench/4273f6877d82bd0b2fa476d1b2f34d121cbccc70/README.md" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "ucc-research-protocol-foldbench-dna-monomer", "kind": "protocol", "name": "FoldBench dna-monomer published full-set assessment", "status": "source_checked", "url": "/database/protocol/ucc-research-protocol-foldbench-dna-monomer/", "evaluations": 5, "metric_rows": 20, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "ucc-research-source-foldbench-paper", "ucc-research-source-foldbench-supp", "ucc-research-source-foldbench-code" ], "source_urls": [ "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12800276/fullTextXML", "https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-025-67127-3/MediaObjects/41467_2025_67127_MOESM1_ESM.pdf", "https://raw.githubusercontent.com/BEAM-Labs/FoldBench/4273f6877d82bd0b2fa476d1b2f34d121cbccc70/README.md" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "ucc-research-protocol-foldbench-protein-dna", "kind": "protocol", "name": "FoldBench protein-dna published full-set assessment", "status": "source_checked", "url": "/database/protocol/ucc-research-protocol-foldbench-protein-dna/", "evaluations": 5, "metric_rows": 20, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "ucc-research-source-foldbench-paper", "ucc-research-source-foldbench-supp", "ucc-research-source-foldbench-code" ], "source_urls": [ "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12800276/fullTextXML", "https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-025-67127-3/MediaObjects/41467_2025_67127_MOESM1_ESM.pdf", "https://raw.githubusercontent.com/BEAM-Labs/FoldBench/4273f6877d82bd0b2fa476d1b2f34d121cbccc70/README.md" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "ucc-research-protocol-foldbench-protein-ligand", "kind": "protocol", "name": "FoldBench protein-ligand published full-set assessment", "status": "source_checked", "url": "/database/protocol/ucc-research-protocol-foldbench-protein-ligand/", "evaluations": 5, "metric_rows": 15, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "ucc-research-source-foldbench-paper", "ucc-research-source-foldbench-supp", "ucc-research-source-foldbench-code" ], "source_urls": [ "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12800276/fullTextXML", "https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-025-67127-3/MediaObjects/41467_2025_67127_MOESM1_ESM.pdf", "https://raw.githubusercontent.com/BEAM-Labs/FoldBench/4273f6877d82bd0b2fa476d1b2f34d121cbccc70/README.md" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. 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Individual observations remain in the results table." ] }, { "id": "atom3d-task-smp-u0at", "kind": "task", "name": "ATOM3D SMP-U0AT: Small molecule properties, atomization energy", "status": "source_checked", "url": "/database/task/atom3d-task-smp-u0at/", "evaluations": 5, "metric_rows": 5, "charts": 1, "charted_metric_rows": 5, "chart_protocol_ids": [ "atom3d-task-smp-u0at" ], "state": "charts_available", "source_ids": [ "evidence-expansion-atom3d-92656c20" ], "source_urls": [ "https://arxiv.org/pdf/2012.04035v4" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "catalog-task-microbial-promoters", "kind": "task", "name": "Bacterial promoter prediction", "status": "discovered", "url": "/database/task/catalog-task-microbial-promoters/", "evaluations": 0, "metric_rows": 0, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_not_yet_collected", "source_ids": [ "catalog-source-prokbert", "catalog-source-evo-2", "expansion-p3-prokbert", "evidence-official-2efbfaba5a1c09f4f7fa" ], "source_urls": [ "https://github.com/nbrg-ppcu/prokbert", "https://github.com/ArcInstitute/evo2", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10810988/fullTextXML", "https://github.com/nbrg-ppcu/prokbert/blob/8670ae92b816cff158a0b85647a8dea122e251eb/README.md" ], "research_status": "broad_task_primary_protocol_linked", "research_review_date": "2026-09-17", "gaps": [ "Broad bacterial promoter prediction includes other organisms and dataset constructions; one E. coli table is not a universal ranking." ] }, { "id": "catalog-task-cell-batch-integration", "kind": "task", "name": "Batch integration", "status": "discovered", "url": "/database/task/catalog-task-cell-batch-integration/", "evaluations": 0, "metric_rows": 0, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_not_yet_collected", "source_ids": [ "catalog-source-scgpt", "catalog-source-scvi", "evidence-expansion-p2-evidence-discovery-final-scib-f65dd8b63336", "src-discovery-theislab-scib" ], "source_urls": [ "https://github.com/bowang-lab/scGPT", "https://github.com/scverse/scvi-tools", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC8748196/fullTextXML", "https://github.com/theislab/scib/blob/cd67913396b4c0430710b3d90f1d1841f5fa4468/README.md" ], "research_status": "broad_task_requires_concrete_protocol_links", "research_review_date": "2026-09-17", "gaps": [ "Bio-conservation and batch-removal components depend on datasets and preprocessing. 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do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "reported-task-4df1fb456d3deb", "kind": "task", "name": "Cell-type structure in frozen embeddings", "status": "needs_review", "url": "/database/task/reported-task-4df1fb456d3deb/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "genept-2024", "evidence-expansion-genept-2024-230a2ec5", "evidence-task-final-a-pmc9556750-xml", "evidence-task-final-a-pmc7331607-xml", "evidence-task-final-a-pmc6731122-xml" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC10614824/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC10614824/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9556750/fullTextXML", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC7331607/fullTextXML", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC6731122/fullTextXML" ], "research_status": "primary_comparison_tables_located", "research_review_date": "2026-09-17", "gaps": [ "complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; 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Five methods for assignedUTRrow; othervariantclasses remain separate. Alignment-aware versus sequence-only inputs explicit; no architecture equivalence inferred. Structured extraction pending." ] }, { "id": "reported-task-7efe245cc94ee5", "kind": "task", "name": "Combinatorial cell-label classification", "status": "needs_review", "url": "/database/task/reported-task-7efe245cc94ee5/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "cell2sentence-2024", "expansion-p3-cell2sentence-2024" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC11565894/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC11565894/" ], "research_status": "primary_comparison_table_screened", "research_review_date": "2026-09-17", "gaps": [ "Partial-credit and full-label metrics cannot share a ranking; keep dataset and label regime explicit.", "Version is the archived preprint, not a later model family release." ] }, { "id": "catalog-task-community-profiling", "kind": "task", "name": "Community profiling", "status": "discovered", "url": "/database/task/catalog-task-community-profiling/", "evaluations": 0, "metric_rows": 0, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_not_yet_collected", "source_ids": [ "catalog-source-metaphlan", "evidence-expansion-p2-evidence-discovery-final-cami2-da932c1cde8b", "evidence-expansion-p2-evidence-discovery-final-opal-a4503ef32e99", "src-discovery-cami-challenge-opal" ], "source_urls": [ "https://github.com/biobakery/MetaPhlAn", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9007738/fullTextXML", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC6398228/fullTextXML", "https://github.com/CAMI-challenge/OPAL/blob/98120c326eef08e391899e4bd3a362e0e6558b4a/README.md" ], "research_status": "broad_task_requires_concrete_protocol_links", "research_review_date": "2026-09-17", "gaps": [ "OPAL is an evaluator rather than a single dataset. Numerical comparisons require selected community dataset, taxonomic rank and profiling output version. No complete main-text score matrix; source data remains pending." ] }, { "id": "reported-task-167f08013c270e", "kind": "task", "name": "Cross-dataset single-cell drug response transfer", "status": "needs_review", "url": "/database/task/reported-task-167f08013c270e/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "scxdr-2026", "expansion-p3-scxdr-2026", "evidence-task-final-a-scxdr-2026-42003-2025-9418-moesm1-esm-pdf", "evidence-task-final-a-gse134839-soft", "evidence-task-final-a-gse149214-soft", "evidence-task-final-a-gse108394-soft", "evidence-task-final-a-gse164614-soft", "evidence-task-final-a-gse230538-soft", "evidence-task-final-a-gse117872-soft", "evidence-task-final-a-gse127298-soft", "evidence-task-final-a-gse140440-soft", "evidence-task-final-a-gse147326-soft" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12859067/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12859067/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12859067/supplementaryFiles", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134839&targ=self&form=text&view=quick", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE149214&targ=self&form=text&view=quick", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE108394&targ=self&form=text&view=quick", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE164614&targ=self&form=text&view=quick", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230538&targ=self&form=text&view=quick", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117872&targ=self&form=text&view=quick", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE127298&targ=self&form=text&view=quick", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE140440&targ=self&form=text&view=quick", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE147326&targ=self&form=text&view=quick" ], "research_status": "primary_comparison_table_screened", "research_review_date": "2026-09-17", "gaps": [ "Keep bulk and single-cell settings explicit; do not call this feature-unseen inductive transfer.", "Standard deviations are printed; resolve exact aggregation population from scenario-level source data before attaching seed-count error bars." ] }, { "id": "reported-task-d82b6284f3f431", "kind": "task", "name": "Cross-platform scATAC cell-type annotation", "status": "needs_review", "url": "/database/task/reported-task-d82b6284f3f431/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "scatac-llmda-2026", "expansion-p3-scatac-llmda-2026" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC13132462/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC13132462/" ], "research_status": "primary_comparison_table_screened", "research_review_date": "2026-09-17", "gaps": [ "Reference-to-query direction is part of protocol identity; reversed pairs are not replicates.", "Inputs and adaptation differ across baselines; scJoint uses scATAC at both stages and Cellcano follows its original target-size-dependent rounds.", "No uncertainty in tables; F1 and accuracy printed separately, including slash-joined Table 3 cells." ] }, { "id": "reported-task-3109f8d0f2b7b5", "kind": "task", "name": "cross-species conservation prediction", "status": "needs_review", "url": "/database/task/reported-task-3109f8d0f2b7b5/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "plantcad2-2025", "expansion-p3-plantcad2-2025", "evidence-task-final-a-plantcad2-2025-media-1-xlsx" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12425018/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12425018/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12425018/supplementaryFiles" ], "research_status": "primary_comparison_table_screened", "research_review_date": "2026-09-17", "gaps": [ "Table 1 is not a complete baseline comparison: named full-baseline scores are in Fig. 2/source workbook. Do not invent model identities from 'best benchmark'.", "Keep lower PlantCAD2 non-TIS score as printed." ] }, { "id": "dart-eval-task-ca-auroc-gm12878", "kind": "task", "name": "DART-Eval CA-AUROC-GM12878: Chromatin activity prediction, GM12878, positives against negatives", "status": "source_checked", "url": "/database/task/dart-eval-task-ca-auroc-gm12878/", "evaluations": 13, "metric_rows": 13, "charts": 1, "charted_metric_rows": 13, "chart_protocol_ids": [ "dart-eval-task-ca-auroc-gm12878" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55" ], "source_urls": [ "https://arxiv.org/html/2412.05430v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "dart-eval-task-ca-auroc-h1esc", "kind": "task", "name": "DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives", "status": "source_checked", "url": "/database/task/dart-eval-task-ca-auroc-h1esc/", "evaluations": 13, "metric_rows": 13, "charts": 1, "charted_metric_rows": 13, "chart_protocol_ids": [ "dart-eval-task-ca-auroc-h1esc" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55" ], "source_urls": [ "https://arxiv.org/html/2412.05430v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "dart-eval-task-ca-auroc-hepg2", "kind": "task", "name": "DART-Eval CA-AUROC-HEPG2: Chromatin activity prediction, HEPG2, positives against negatives", "status": "source_checked", "url": "/database/task/dart-eval-task-ca-auroc-hepg2/", "evaluations": 13, "metric_rows": 13, "charts": 1, "charted_metric_rows": 13, "chart_protocol_ids": [ "dart-eval-task-ca-auroc-hepg2" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55" ], "source_urls": [ "https://arxiv.org/html/2412.05430v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "dart-eval-task-ca-auroc-imr90", "kind": "task", "name": "DART-Eval CA-AUROC-IMR90: Chromatin activity prediction, IMR90, positives against negatives", "status": "source_checked", "url": "/database/task/dart-eval-task-ca-auroc-imr90/", "evaluations": 13, "metric_rows": 13, "charts": 1, "charted_metric_rows": 13, "chart_protocol_ids": [ "dart-eval-task-ca-auroc-imr90" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55" ], "source_urls": [ "https://arxiv.org/html/2412.05430v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "dart-eval-task-ca-auroc-k562", "kind": "task", "name": "DART-Eval CA-AUROC-K562: Chromatin activity prediction, K562, positives against negatives", "status": "source_checked", "url": "/database/task/dart-eval-task-ca-auroc-k562/", "evaluations": 13, "metric_rows": 13, "charts": 1, "charted_metric_rows": 13, "chart_protocol_ids": [ "dart-eval-task-ca-auroc-k562" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55" ], "source_urls": [ "https://arxiv.org/html/2412.05430v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "dart-eval-task-ca-spearman-gm12878", "kind": "task", "name": "DART-Eval CA-SPEARMAN-GM12878: Chromatin activity prediction, GM12878, positives only", "status": "source_checked", "url": "/database/task/dart-eval-task-ca-spearman-gm12878/", "evaluations": 13, "metric_rows": 13, "charts": 1, "charted_metric_rows": 13, "chart_protocol_ids": [ "dart-eval-task-ca-spearman-gm12878" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55" ], "source_urls": [ "https://arxiv.org/html/2412.05430v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "dart-eval-task-ca-spearman-h1esc", "kind": "task", "name": "DART-Eval CA-SPEARMAN-H1ESC: Chromatin activity prediction, H1ESC, positives only", "status": "source_checked", "url": "/database/task/dart-eval-task-ca-spearman-h1esc/", "evaluations": 13, "metric_rows": 13, "charts": 1, "charted_metric_rows": 13, "chart_protocol_ids": [ "dart-eval-task-ca-spearman-h1esc" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55" ], "source_urls": [ "https://arxiv.org/html/2412.05430v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "dart-eval-task-ca-spearman-hepg2", "kind": "task", "name": "DART-Eval CA-SPEARMAN-HEPG2: Chromatin activity prediction, HEPG2, positives only", "status": "source_checked", "url": "/database/task/dart-eval-task-ca-spearman-hepg2/", "evaluations": 13, "metric_rows": 13, "charts": 1, "charted_metric_rows": 13, "chart_protocol_ids": [ "dart-eval-task-ca-spearman-hepg2" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55" ], "source_urls": [ "https://arxiv.org/html/2412.05430v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "dart-eval-task-ca-spearman-imr90", "kind": "task", "name": "DART-Eval CA-SPEARMAN-IMR90: Chromatin activity prediction, IMR90, positives only", "status": "source_checked", "url": "/database/task/dart-eval-task-ca-spearman-imr90/", "evaluations": 13, "metric_rows": 13, "charts": 1, "charted_metric_rows": 13, "chart_protocol_ids": [ "dart-eval-task-ca-spearman-imr90" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55" ], "source_urls": [ "https://arxiv.org/html/2412.05430v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "dart-eval-task-ca-spearman-k562", "kind": "task", "name": "DART-Eval CA-SPEARMAN-K562: Chromatin activity prediction, K562, positives only", "status": "source_checked", "url": "/database/task/dart-eval-task-ca-spearman-k562/", "evaluations": 13, "metric_rows": 13, "charts": 1, "charted_metric_rows": 13, "chart_protocol_ids": [ "dart-eval-task-ca-spearman-k562" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55" ], "source_urls": [ "https://arxiv.org/html/2412.05430v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "dart-eval-task-cts-acc", "kind": "task", "name": "DART-Eval CTS-ACC: Cell-type-specific element classification, overall accuracy", "status": "source_checked", "url": "/database/task/dart-eval-task-cts-acc/", "evaluations": 14, "metric_rows": 14, "charts": 1, "charted_metric_rows": 14, "chart_protocol_ids": [ "dart-eval-task-cts-acc" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55" ], "source_urls": [ "https://arxiv.org/html/2412.05430v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "dart-eval-task-cts-gm12878", "kind": "task", "name": "DART-Eval CTS-GM12878: Cell-type-specific element classification, GM12878", "status": "source_checked", "url": "/database/task/dart-eval-task-cts-gm12878/", "evaluations": 14, "metric_rows": 14, "charts": 1, "charted_metric_rows": 14, "chart_protocol_ids": [ "dart-eval-task-cts-gm12878" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55" ], "source_urls": [ "https://arxiv.org/html/2412.05430v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "dart-eval-task-cts-h1esc", "kind": "task", "name": "DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC", "status": "source_checked", "url": "/database/task/dart-eval-task-cts-h1esc/", "evaluations": 14, "metric_rows": 14, "charts": 1, "charted_metric_rows": 14, "chart_protocol_ids": [ "dart-eval-task-cts-h1esc" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55" ], "source_urls": [ "https://arxiv.org/html/2412.05430v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "dart-eval-task-cts-hepg2", "kind": "task", "name": "DART-Eval CTS-HEPG2: Cell-type-specific element classification, HEPG2", "status": "source_checked", "url": "/database/task/dart-eval-task-cts-hepg2/", "evaluations": 14, "metric_rows": 14, "charts": 1, "charted_metric_rows": 14, "chart_protocol_ids": [ "dart-eval-task-cts-hepg2" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55" ], "source_urls": [ "https://arxiv.org/html/2412.05430v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "dart-eval-task-cts-imr90", "kind": "task", "name": "DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90", "status": "source_checked", "url": "/database/task/dart-eval-task-cts-imr90/", "evaluations": 14, "metric_rows": 14, "charts": 1, "charted_metric_rows": 14, "chart_protocol_ids": [ "dart-eval-task-cts-imr90" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55" ], "source_urls": [ "https://arxiv.org/html/2412.05430v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "dart-eval-task-cts-k562", "kind": "task", "name": "DART-Eval CTS-K562: Cell-type-specific element classification, K562", "status": "source_checked", "url": "/database/task/dart-eval-task-cts-k562/", "evaluations": 14, "metric_rows": 14, "charts": 1, "charted_metric_rows": 14, "chart_protocol_ids": [ "dart-eval-task-cts-k562" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55" ], "source_urls": [ "https://arxiv.org/html/2412.05430v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "dart-eval-task-rei-abs", "kind": "task", "name": "DART-Eval REI-ABS: Regulatory element identification, absolute accuracy", "status": "source_checked", "url": "/database/task/dart-eval-task-rei-abs/", "evaluations": 13, "metric_rows": 13, "charts": 1, "charted_metric_rows": 13, "chart_protocol_ids": [ "dart-eval-task-rei-abs" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55" ], "source_urls": [ "https://arxiv.org/html/2412.05430v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "dart-eval-task-rei-acc", "kind": "task", "name": "DART-Eval REI-ACC: Regulatory element identification, zero-shot accuracy", "status": "source_checked", "url": "/database/task/dart-eval-task-rei-acc/", "evaluations": 6, "metric_rows": 6, "charts": 1, "charted_metric_rows": 6, "chart_protocol_ids": [ "dart-eval-task-rei-acc" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55" ], "source_urls": [ "https://arxiv.org/html/2412.05430v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "dart-eval-task-rei-pair", "kind": "task", "name": "DART-Eval REI-PAIR: Regulatory element identification, paired accuracy", "status": "source_checked", "url": "/database/task/dart-eval-task-rei-pair/", "evaluations": 13, "metric_rows": 13, "charts": 1, "charted_metric_rows": 13, "chart_protocol_ids": [ "dart-eval-task-rei-pair" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55" ], "source_urls": [ "https://arxiv.org/html/2412.05430v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "dart-eval-task-vs-african-auroc", "kind": "task", "name": "DART-Eval VS-AFRICAN-AUROC: Variant scoring on Chromatin QTLs in African LCLs, AUROC", "status": "source_checked", "url": "/database/task/dart-eval-task-vs-african-auroc/", "evaluations": 22, "metric_rows": 22, "charts": 1, "charted_metric_rows": 22, "chart_protocol_ids": [ "dart-eval-task-vs-african-auroc" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55" ], "source_urls": [ "https://arxiv.org/html/2412.05430v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "dart-eval-task-vs-african-pearson-r", "kind": "task", "name": "DART-Eval VS-AFRICAN-PEARSON_R: Variant scoring on Chromatin QTLs in African LCLs, Pearson r", "status": "source_checked", "url": "/database/task/dart-eval-task-vs-african-pearson-r/", "evaluations": 13, "metric_rows": 13, "charts": 1, "charted_metric_rows": 13, "chart_protocol_ids": [ "dart-eval-task-vs-african-pearson-r" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55" ], "source_urls": [ "https://arxiv.org/html/2412.05430v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "dart-eval-task-vs-yoruban-auroc", "kind": "task", "name": "DART-Eval VS-YORUBAN-AUROC: Variant scoring on DNase QTLs in Yoruban LCLs, AUROC", "status": "source_checked", "url": "/database/task/dart-eval-task-vs-yoruban-auroc/", "evaluations": 22, "metric_rows": 22, "charts": 1, "charted_metric_rows": 22, "chart_protocol_ids": [ "dart-eval-task-vs-yoruban-auroc" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55" ], "source_urls": [ "https://arxiv.org/html/2412.05430v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "dart-eval-task-vs-yoruban-pearson-r", "kind": "task", "name": "DART-Eval VS-YORUBAN-PEARSON_R: Variant scoring on DNase QTLs in Yoruban LCLs, Pearson r", "status": "source_checked", "url": "/database/task/dart-eval-task-vs-yoruban-pearson-r/", "evaluations": 13, "metric_rows": 13, "charts": 1, "charted_metric_rows": 13, "chart_protocol_ids": [ "dart-eval-task-vs-yoruban-pearson-r" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55" ], "source_urls": [ "https://arxiv.org/html/2412.05430v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "reported-task-003d746a129c9b", "kind": "task", "name": "differentially expressed gene identification", "status": "needs_review", "url": "/database/task/reported-task-003d746a129c9b/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "insilico-perturbation-auprc-2025", "expansion-p3-insilico-perturbation-auprc-2025" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12400816/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12400816/" ], "research_status": "primary_comparison_table_screened", "research_review_date": "2026-09-17", "gaps": [ "Do not pool cell types or recall thresholds; table gives no uncertainty for these cells." ] }, { "id": "reported-task-9917a0e69f33e7", "kind": "task", "name": "DNA-binding residue prediction", "status": "needs_review", "url": "/database/task/reported-task-9917a0e69f33e7/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "megsite-2025", "evidence-expansion-p2-megsite-2025-10d131223318" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12496013/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12496013/fullTextXML" ], "research_status": "source_found_structured_extraction_pending", "research_review_date": "2026-09-17", "gaps": [ "Complete raw table acquired. Assigned benchmark is DNA-binding; RNA cohorts need distinct protocols. PCC-to-MegSite agreement and associatedPvalues are not predictive performance. Structured extraction pending." ] }, { "id": "reported-task-d6018ca598e525", "kind": "task", "name": "Donor-aware age-class prediction", "status": "needs_review", "url": "/database/task/reported-task-d6018ca598e525/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "single-cell-aging-probes-2026", "evidence-expansion-p2-single-cell-aging-probes-2026-d6cfb13933ce" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC13407579/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13407579/fullTextXML" ], "research_status": "source_found_structured_extraction_pending", "research_review_date": "2026-09-17", "gaps": [ "Complete raw comparison acquired. Best-scFM is a selected pipeline, not a named family by inference. PCA, permutation mean/p 95 and chance 1/K remain separate reference types. Structured extraction pending." ] }, { "id": "catalog-task-cell-reference-mapping", "kind": "task", "name": "Donor-held-out reference mapping", "status": "discovered", "url": "/database/task/catalog-task-cell-reference-mapping/", "evaluations": 0, "metric_rows": 0, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_not_yet_collected", "source_ids": [ "catalog-source-geneformer", "catalog-source-scgpt", "catalog-source-scfoundation", "catalog-source-scvi", "expansion-p3-open-problems", "expansion-p3-open-problems-paper", "expansion-p3-scanvi", "evidence-official-0cbab80c2d1769287a1f", "src-discovery-theislab-scib" ], "source_urls": [ "https://huggingface.co/ctheodoris/Geneformer", "https://github.com/bowang-lab/scGPT", "https://github.com/biomap-research/scFoundation", "https://github.com/scverse/scvi-tools", "https://www.openproblems.bio/benchmarks/label_projection/v1.0.0/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11030530/fullTextXML", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC7829634/fullTextXML", "https://github.com/scverse/scvi-tools/blob/73b28e44223621470e582a81a102c107bb22678b/docs/user_guide/models/scvi.md", "https://github.com/theislab/scib/blob/cd67913396b4c0430710b3d90f1d1841f5fa4468/README.md" ], "research_status": "broad_task_primary_protocol_linked", "research_review_date": "2026-09-17", "gaps": [ "A split by batch/reference is not automatically a donor-held-out split. A chart needs the exact dataset donor manifest.", "Open Problems controls and normalization choices must remain separate from raw label accuracy/F1." ] }, { "id": "reported-task-3891811dcce8b3", "kind": "task", "name": "E. coli sigma70 promoter prediction", "status": "needs_review", "url": "/database/task/reported-task-3891811dcce8b3/", "evaluations": 15, "metric_rows": 60, "charts": 4, "charted_metric_rows": 60, "chart_protocol_ids": [ "paper-protocol-94fa3494d41bcd98d2" ], "state": "charts_available", "source_ids": [ "prokbert-2024", "part2-prokbert-2024" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC10810988/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10810988/fullTextXML" ], "research_status": "complete_comparison_tables_extracted_pending_publication_review", "research_review_date": "2026-09-17", "gaps": [ "Independent batch review before import; preserve existing observation identities." ] }, { "id": "reported-task-e5c34f686ac403", "kind": "task", "name": "E. coli sigma70 promoter prediction", "status": "needs_review", "url": "/database/task/reported-task-e5c34f686ac403/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "cyaprombert-2022", "evidence-expansion-cyaprombert-2022-74278ccd" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC9745317/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC9745317/" ], "research_status": "primary_comparison_tables_located", "research_review_date": "2026-09-17", "gaps": [ "complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.", "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "catalog-task-enhancer-effects", "kind": "task", "name": "Enhancer / MPRA effects", "status": "discovered", "url": "/database/task/catalog-task-enhancer-effects/", "evaluations": 0, "metric_rows": 0, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_not_yet_collected", "source_ids": [ "catalog-source-dnabert-2", "catalog-source-nt-v2", "catalog-source-evo-2", "catalog-source-alphagenome", "evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55", "src-discovery-kundajelab-dart-eval", "dart-eval-regulatory-2024" ], "source_urls": [ "https://huggingface.co/zhihan1996/DNABERT-2-117M", "https://huggingface.co/InstaDeepAI/nucleotide-transformer-v2-50m-multi-species", "https://github.com/ArcInstitute/evo2", "https://github.com/google-deepmind/alphagenome_research", "https://arxiv.org/html/2412.05430v1", "https://github.com/kundajelab/DART-Eval/blob/af2a86d666c35304257c2fa7e15180e1fbcabb01/README.md", "https://proceedings.neurips.cc/paper_files/paper/2024/file/71998bfc3217ffe1cca1ee084dfadadd-Paper-Datasets_and_Benchmarks_Track.pdf" ], "research_status": "broad_task_requires_concrete_protocol_links", "research_review_date": "2026-09-17", "gaps": [ "Regulatory sequence detection, TF motifs, cell-type activity and variant effects are distinct protocols. Enhancer broad-task record must link concrete tasks, not inherit every DART result. Existing DART observations require source-cell identity reuse." ] }, { "id": "reported-task-132da895d4c381", "kind": "task", "name": "Enhancer classification", "status": "needs_review", "url": "/database/task/reported-task-132da895d4c381/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "enbed-2024", "evidence-expansion-enbed-2024-e95d4be7", "evidence-task-final-a-enbed-2024-vbae117-supplementary-data-pdf" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC11341122/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC11341122/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11341122/supplementaryFiles" ], "research_status": "primary_comparison_tables_located", "research_review_date": "2026-09-17", "gaps": [ "complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.", "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "reported-task-22024610c4d658", "kind": "task", "name": "enhancer prediction", "status": "needs_review", "url": "/database/task/reported-task-22024610c4d658/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "hi-enhancer-2025", "expansion-p3-hi-enhancer-2025", "evidence-task-final-a-hi-enhancer-2025-btaf441-supplementary-data-docx" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12758598/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12758598/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12758598/supplementaryFiles" ], "research_status": "primary_comparison_table_screened", "research_review_date": "2026-09-17", "gaps": [ "Text S6 defines the independent test set; supplementary data is necessary for a complete dataset manifest.", "Table 2 does not report replicate uncertainty; other-method provenance must retain paper citations rather than imply all were rerun." ] }, { "id": "reported-task-64607443a9ba15", "kind": "task", "name": "enhancer prediction", "status": "needs_review", "url": "/database/task/reported-task-64607443a9ba15/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "enhancer-position-encoding-2024", "expansion-p3-enhancer-position-encoding-2024" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC11167433/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC11167433/" ], "research_status": "primary_comparison_table_screened", "research_review_date": "2026-09-17", "gaps": [ "Published Fig. 5/6 advanced-model comparisons require figure/source-data review; do not pretend Table 3 gives scores.", "Avoid mixing human and mouse populations or treating source-level similarity filtering as an exact split manifest." ] }, { "id": "reported-task-86a628af87ff8f", "kind": "task", "name": "enhancer recognition", "status": "needs_review", "url": "/database/task/reported-task-86a628af87ff8f/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "dnabert2-enhancer-2025", "evidence-expansion-dnabert2-enhancer-2025-d052b80e" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC11981215/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC11981215/" ], "research_status": "primary_comparison_tables_located", "research_review_date": "2026-09-17", "gaps": [ "complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.", "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "reported-task-2cbac97dd849f5", "kind": "task", "name": "Enhancer-target gene prediction", "status": "needs_review", "url": "/database/task/reported-task-2cbac97dd849f5/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "dnalongbench-2025", "evidence-expansion-dnalongbench-2025-fa440a17" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC11741265/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC11741265/" ], "research_status": "primary_comparison_tables_located", "research_review_date": "2026-09-17", "gaps": [ "complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.", "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "reported-task-1ebf9b408517f9", "kind": "task", "name": "Enzyme functional identity prediction", "status": "needs_review", "url": "/database/task/reported-task-1ebf9b408517f9/", "evaluations": 5, "metric_rows": 40, "charts": 8, "charted_metric_rows": 40, "chart_protocol_ids": [ "paper-protocol-7088bcc2f0033b8a29" ], "state": "charts_available", "source_ids": [ "fujisan-2024", "part2-fujisan-2024" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC11609699/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11609699/fullTextXML" ], "research_status": "complete_comparison_tables_extracted_pending_publication_review", "research_review_date": "2026-09-17", "gaps": [ "Independent batch review before import; preserve existing observation identities." ] }, { "id": "reported-task-c40dac20d9af66", "kind": "task", "name": "extremely long RNA species classification", "status": "needs_review", "url": "/database/task/reported-task-c40dac20d9af66/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "birna-bert-2025", "expansion-p3-birna-bert-2025", "evidence-task-final-b-birna-supplement" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12635123/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12635123/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12635123/supplementaryFiles" ], "research_status": "primary_comparison_table_screened", "research_review_date": "2026-09-17", "gaps": [ "No uncertainty in Table 2; exact long-sequence window/aggregation details remain tied to this paper's downstream classifiers.", "Species classification scores do not measure RNA-structure accuracy." ] }, { "id": "flip-task-aav-1-vs-rest", "kind": "task", "name": "FLIP AAV-1-VS-REST: AAV fitness prediction, 1-vs-rest split", "status": "source_checked", "url": "/database/task/flip-task-aav-1-vs-rest/", "evaluations": 12, "metric_rows": 12, "charts": 1, "charted_metric_rows": 12, "chart_protocol_ids": [ "flip-task-aav-1-vs-rest" ], "state": "charts_available", "source_ids": [ "expansion-p3-flip" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_2021_manuscript.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "flip-task-aav-2-vs-rest", "kind": "task", "name": "FLIP AAV-2-VS-REST: AAV fitness prediction, 2-vs-rest split", "status": "source_checked", "url": "/database/task/flip-task-aav-2-vs-rest/", "evaluations": 12, "metric_rows": 12, "charts": 1, "charted_metric_rows": 12, "chart_protocol_ids": [ "flip-task-aav-2-vs-rest" ], "state": "charts_available", "source_ids": [ "expansion-p3-flip" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_2021_manuscript.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "flip-task-aav-7-vs-rest", "kind": "task", "name": "FLIP AAV-7-VS-REST: AAV fitness prediction, 7-vs-rest split", "status": "source_checked", "url": "/database/task/flip-task-aav-7-vs-rest/", "evaluations": 12, "metric_rows": 12, "charts": 1, "charted_metric_rows": 12, "chart_protocol_ids": [ "flip-task-aav-7-vs-rest" ], "state": "charts_available", "source_ids": [ "expansion-p3-flip" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_2021_manuscript.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "flip-task-aav-des-mut", "kind": "task", "name": "FLIP AAV-DES-MUT: AAV fitness prediction, Des-Mut split", "status": "source_checked", "url": "/database/task/flip-task-aav-des-mut/", "evaluations": 9, "metric_rows": 9, "charts": 1, "charted_metric_rows": 9, "chart_protocol_ids": [ "flip-task-aav-des-mut" ], "state": "charts_available", "source_ids": [ "expansion-p3-flip" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_2021_manuscript.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. 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Individual observations remain in the results table." ] }, { "id": "flip-task-gb1-2-vs-rest", "kind": "task", "name": "FLIP GB1-2-VS-REST: GB1 fitness prediction, 2-vs-rest split", "status": "source_checked", "url": "/database/task/flip-task-gb1-2-vs-rest/", "evaluations": 13, "metric_rows": 13, "charts": 1, "charted_metric_rows": 13, "chart_protocol_ids": [ "flip-task-gb1-2-vs-rest" ], "state": "charts_available", "source_ids": [ "expansion-p3-flip" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_2021_manuscript.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "flip-task-gb1-3-vs-rest", "kind": "task", "name": "FLIP GB1-3-VS-REST: GB1 fitness prediction, 3-vs-rest split", "status": "source_checked", "url": "/database/task/flip-task-gb1-3-vs-rest/", "evaluations": 13, "metric_rows": 13, "charts": 1, "charted_metric_rows": 13, "chart_protocol_ids": [ "flip-task-gb1-3-vs-rest" ], "state": "charts_available", "source_ids": [ "expansion-p3-flip" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_2021_manuscript.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "flip-task-gb1-low-vs-high", "kind": "task", "name": "FLIP GB1-LOW-VS-HIGH: GB1 fitness prediction, low-vs-high split", "status": "source_checked", "url": "/database/task/flip-task-gb1-low-vs-high/", "evaluations": 13, "metric_rows": 13, "charts": 1, "charted_metric_rows": 13, "chart_protocol_ids": [ "flip-task-gb1-low-vs-high" ], "state": "charts_available", "source_ids": [ "expansion-p3-flip" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_2021_manuscript.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "flip-task-random-sampled-splits-aav", "kind": "task", "name": "FLIP RANDOM-SAMPLED-SPLITS-AAV: Random sampled splits fitness prediction, AAV split", "status": "source_checked", "url": "/database/task/flip-task-random-sampled-splits-aav/", "evaluations": 5, "metric_rows": 5, "charts": 1, "charted_metric_rows": 5, "chart_protocol_ids": [ "flip-task-random-sampled-splits-aav" ], "state": "charts_available", "source_ids": [ "expansion-p3-flip" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_2021_manuscript.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "flip-task-random-sampled-splits-gb1", "kind": "task", "name": "FLIP RANDOM-SAMPLED-SPLITS-GB1: Random sampled splits fitness prediction, GB1 split", "status": "source_checked", "url": "/database/task/flip-task-random-sampled-splits-gb1/", "evaluations": 5, "metric_rows": 5, "charts": 1, "charted_metric_rows": 5, "chart_protocol_ids": [ "flip-task-random-sampled-splits-gb1" ], "state": "charts_available", "source_ids": [ "expansion-p3-flip" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_2021_manuscript.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "flip-task-thermostability-human-cell", "kind": "task", "name": "FLIP THERMOSTABILITY-HUMAN-CELL: Thermostability fitness prediction, Human-Cell split", "status": "source_checked", "url": "/database/task/flip-task-thermostability-human-cell/", "evaluations": 8, "metric_rows": 8, "charts": 1, "charted_metric_rows": 8, "chart_protocol_ids": [ "flip-task-thermostability-human-cell" ], "state": "charts_available", "source_ids": [ "expansion-p3-flip" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_2021_manuscript.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "flip-task-thermostability-human", "kind": "task", "name": "FLIP THERMOSTABILITY-HUMAN: Thermostability fitness prediction, Human split", "status": "source_checked", "url": "/database/task/flip-task-thermostability-human/", "evaluations": 8, "metric_rows": 8, "charts": 1, "charted_metric_rows": 8, "chart_protocol_ids": [ "flip-task-thermostability-human" ], "state": "charts_available", "source_ids": [ "expansion-p3-flip" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_2021_manuscript.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "flip-task-thermostability-mixed", "kind": "task", "name": "FLIP THERMOSTABILITY-MIXED: Thermostability fitness prediction, Mixed split", "status": "source_checked", "url": "/database/task/flip-task-thermostability-mixed/", "evaluations": 8, "metric_rows": 8, "charts": 1, "charted_metric_rows": 8, "chart_protocol_ids": [ "flip-task-thermostability-mixed" ], "state": "charts_available", "source_ids": [ "expansion-p3-flip" ], "source_urls": [ "https://flip.protein.properties/assets/FLIP_2021_manuscript.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "reported-task-1c74661df2c401", "kind": "task", "name": "flu-vaccine mRNA property prediction", "status": "needs_review", "url": "/database/task/reported-task-1c74661df2c401/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "codonbert-vaccines-2024", "evidence-expansion-codonbert-vaccines-2024-29680737" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC11368176/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC11368176/" ], "research_status": "primary_comparison_tables_located", "research_review_date": "2026-09-17", "gaps": [ "complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.", "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "reported-task-c9d2a6435979e9", "kind": "task", "name": "G-quadruplex classification", "status": "needs_review", "url": "/database/task/reported-task-c9d2a6435979e9/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "quadruplex-llm-benchmark-2025", "evidence-expansion-p2-quadruplex-llm-benchmark-2025-c3d7c6d068d3" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC11953744/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11953744/fullTextXML" ], "research_status": "source_found_structured_extraction_pending", "research_review_date": "2026-09-17", "gaps": [ "Complete raw tables acquired. Positive/negative construction, sequence lengths and train/test splits remain part of each G4 protocol; existing observations preserved. Structured extraction pending." ] }, { "id": "reported-task-ee34721cf55590", "kind": "task", "name": "gene fusion breakpoint classification", "status": "needs_review", "url": "/database/task/reported-task-ee34721cf55590/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "fusion-breakpoint-foundation-models-2026", "expansion-p3-fusion-breakpoint-foundation-models-2026" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC13182013/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC13182013/" ], "research_status": "primary_comparison_table_screened", "research_review_date": "2026-09-17", "gaps": [ "Counts are approximate (~36k train, ~8k validation, ~8k test) and must remain approximate.", "NN values are final-epoch performance; SVM is a single run. No replicate confidence bounds.", "Do not assign embedding-plus-classifier scores to bare foundation-model checkpoints." ] }, { "id": "reported-task-3063ed4da76b4b", "kind": "task", "name": "Gene-regulatory link prediction", "status": "needs_review", "url": "/database/task/reported-task-3063ed4da76b4b/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "scregnet-2025", "evidence-expansion-p2-scregnet-2025-65b3272d47bb" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC11838224/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11838224/fullTextXML" ], "research_status": "source_found_structured_extraction_pending", "research_review_date": "2026-09-17", "gaps": [ "Raw XML stacked AUROC/AUPRC cells preserved with explicit linebreak delimiters. Two GENELink settings must not be conflated. Structured table extraction and exact uncertainty scope remain pending." ] }, { "id": "reported-task-99afd88cb12895", "kind": "task", "name": "gene-regulatory signal prediction", "status": "needs_review", "url": "/database/task/reported-task-99afd88cb12895/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "single-cell-residual-geometry-2026", "expansion-p3-single-cell-residual-geometry-2026" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC13418759/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC13418759/" ], "research_status": "primary_comparison_table_screened", "research_review_date": "2026-09-17", "gaps": [ "Original asymmetric extraction in Table 4 is not a fair matched-input comparison; prefer Table 9 with its single-seed context.", "Strict leave-both-out improvements shrink near zero; do not omit this limitation.", "Source contains rounded deltas and intervals/significance annotations; do not recompute them from rounded absolute numbers." ] }, { "id": "geneb-task-linear-probe", "kind": "task", "name": "GENEB LINEAR-PROBE: Average macro-MCC across the 13 representative tasks, linear probe", "status": "source_checked", "url": "/database/task/geneb-task-linear-probe/", "evaluations": 11, "metric_rows": 11, "charts": 1, "charted_metric_rows": 11, "chart_protocol_ids": [ "geneb-task-linear-probe" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-evidence-discovery-final-geneb-47975089c0ca" ], "source_urls": [ "https://arxiv.org/html/2606.04525v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "geneb-task-mlp-probe", "kind": "task", "name": "GENEB MLP-PROBE: Average macro-MCC across the 13 representative tasks, MLP probe", "status": "source_checked", "url": "/database/task/geneb-task-mlp-probe/", "evaluations": 11, "metric_rows": 11, "charts": 1, "charted_metric_rows": 11, "chart_protocol_ids": [ "geneb-task-mlp-probe" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-evidence-discovery-final-geneb-47975089c0ca" ], "source_urls": [ "https://arxiv.org/html/2606.04525v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "reported-task-dd001540e0f4ec", "kind": "task", "name": "Genome-wide prophage detection", "status": "needs_review", "url": "/database/task/reported-task-dd001540e0f4ec/", "evaluations": 17, "metric_rows": 102, "charts": 6, "charted_metric_rows": 102, "chart_protocol_ids": [ "paper-protocol-41c6e227215346177d" ], "state": "charts_available", "source_ids": [ "lambda-prophage-2026", "part2-lambda-prophage-2026" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC13041943/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13041943/fullTextXML" ], "research_status": "complete_comparison_tables_extracted_pending_publication_review", "research_review_date": "2026-09-17", "gaps": [ "Independent batch review before import; preserve existing observation identities." ] }, { "id": "genomic-benchmarks-task-demo-coding-vs-intergenomic-seqs-accuracy", "kind": "task", "name": "Genomic Benchmarks DEMO-CODING-VS-INTERGENOMIC-SEQS-ACCURACY: demo_coding_vs_intergenomic_seqs, Accuracy", "status": "source_checked", "url": "/database/task/genomic-benchmarks-task-demo-coding-vs-intergenomic-seqs-accuracy/", "evaluations": 2, "metric_rows": 2, "charts": 1, "charted_metric_rows": 2, "chart_protocol_ids": [ "genomic-benchmarks-task-demo-coding-vs-intergenomic-seqs-accuracy" ], "state": "charts_available", "source_ids": [ "expansion-p3-genomic-benchmarks" ], "source_urls": [ "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10150520/fullTextXML" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "genomic-benchmarks-task-demo-coding-vs-intergenomic-seqs-f1", "kind": "task", "name": "Genomic Benchmarks DEMO-CODING-VS-INTERGENOMIC-SEQS-F1: demo_coding_vs_intergenomic_seqs, F1 score", "status": "source_checked", "url": "/database/task/genomic-benchmarks-task-demo-coding-vs-intergenomic-seqs-f1/", "evaluations": 2, "metric_rows": 2, "charts": 1, "charted_metric_rows": 2, "chart_protocol_ids": [ "genomic-benchmarks-task-demo-coding-vs-intergenomic-seqs-f1" ], "state": "charts_available", "source_ids": [ "expansion-p3-genomic-benchmarks" ], "source_urls": [ "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10150520/fullTextXML" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "genomic-benchmarks-task-demo-human-or-worm-accuracy", "kind": "task", "name": "Genomic Benchmarks DEMO-HUMAN-OR-WORM-ACCURACY: demo_human_or_worm, Accuracy", "status": "source_checked", "url": "/database/task/genomic-benchmarks-task-demo-human-or-worm-accuracy/", "evaluations": 2, "metric_rows": 2, "charts": 1, "charted_metric_rows": 2, "chart_protocol_ids": [ "genomic-benchmarks-task-demo-human-or-worm-accuracy" ], "state": "charts_available", "source_ids": [ "expansion-p3-genomic-benchmarks" ], "source_urls": [ "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10150520/fullTextXML" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "genomic-benchmarks-task-demo-human-or-worm-f1", "kind": "task", "name": "Genomic Benchmarks DEMO-HUMAN-OR-WORM-F1: demo_human_or_worm, F1 score", "status": "source_checked", "url": "/database/task/genomic-benchmarks-task-demo-human-or-worm-f1/", "evaluations": 2, "metric_rows": 2, "charts": 1, "charted_metric_rows": 2, "chart_protocol_ids": [ "genomic-benchmarks-task-demo-human-or-worm-f1" ], "state": "charts_available", "source_ids": [ "expansion-p3-genomic-benchmarks" ], "source_urls": [ "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10150520/fullTextXML" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "genomic-benchmarks-task-drosophila-enhancers-stark-accuracy", "kind": "task", "name": "Genomic Benchmarks DROSOPHILA-ENHANCERS-STARK-ACCURACY: drosophila_enhancers_stark, Accuracy", "status": "source_checked", "url": "/database/task/genomic-benchmarks-task-drosophila-enhancers-stark-accuracy/", "evaluations": 2, "metric_rows": 2, "charts": 1, "charted_metric_rows": 2, "chart_protocol_ids": [ "genomic-benchmarks-task-drosophila-enhancers-stark-accuracy" ], "state": "charts_available", "source_ids": [ "expansion-p3-genomic-benchmarks" ], "source_urls": [ "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10150520/fullTextXML" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "genomic-benchmarks-task-drosophila-enhancers-stark-f1", "kind": "task", "name": "Genomic Benchmarks DROSOPHILA-ENHANCERS-STARK-F1: drosophila_enhancers_stark, F1 score", "status": "source_checked", "url": "/database/task/genomic-benchmarks-task-drosophila-enhancers-stark-f1/", "evaluations": 2, "metric_rows": 2, "charts": 1, "charted_metric_rows": 2, "chart_protocol_ids": [ "genomic-benchmarks-task-drosophila-enhancers-stark-f1" ], "state": "charts_available", "source_ids": [ "expansion-p3-genomic-benchmarks" ], "source_urls": [ "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10150520/fullTextXML" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "genomic-benchmarks-task-dummy-mouse-enhancers-ensembl-accuracy", "kind": "task", "name": "Genomic Benchmarks DUMMY-MOUSE-ENHANCERS-ENSEMBL-ACCURACY: dummy_mouse_enhancers_ensembl, Accuracy", "status": "source_checked", "url": "/database/task/genomic-benchmarks-task-dummy-mouse-enhancers-ensembl-accuracy/", "evaluations": 2, "metric_rows": 2, "charts": 1, "charted_metric_rows": 2, "chart_protocol_ids": [ "genomic-benchmarks-task-dummy-mouse-enhancers-ensembl-accuracy" ], "state": "charts_available", "source_ids": [ "expansion-p3-genomic-benchmarks" ], "source_urls": [ "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10150520/fullTextXML" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "genomic-benchmarks-task-dummy-mouse-enhancers-ensembl-f1", "kind": "task", "name": "Genomic Benchmarks DUMMY-MOUSE-ENHANCERS-ENSEMBL-F1: dummy_mouse_enhancers_ensembl, F1 score", "status": "source_checked", "url": "/database/task/genomic-benchmarks-task-dummy-mouse-enhancers-ensembl-f1/", "evaluations": 2, "metric_rows": 2, "charts": 1, "charted_metric_rows": 2, "chart_protocol_ids": [ "genomic-benchmarks-task-dummy-mouse-enhancers-ensembl-f1" ], "state": "charts_available", "source_ids": [ "expansion-p3-genomic-benchmarks" ], "source_urls": [ "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10150520/fullTextXML" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "genomic-benchmarks-task-human-enhancers-cohn-accuracy", "kind": "task", "name": "Genomic Benchmarks HUMAN-ENHANCERS-COHN-ACCURACY: human_enhancers_cohn, Accuracy", "status": "source_checked", "url": "/database/task/genomic-benchmarks-task-human-enhancers-cohn-accuracy/", "evaluations": 2, "metric_rows": 2, "charts": 1, "charted_metric_rows": 2, "chart_protocol_ids": [ "genomic-benchmarks-task-human-enhancers-cohn-accuracy" ], "state": "charts_available", "source_ids": [ "expansion-p3-genomic-benchmarks" ], "source_urls": [ "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10150520/fullTextXML" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "genomic-benchmarks-task-human-enhancers-cohn-f1", "kind": "task", "name": "Genomic Benchmarks HUMAN-ENHANCERS-COHN-F1: human_enhancers_cohn, F1 score", "status": "source_checked", "url": "/database/task/genomic-benchmarks-task-human-enhancers-cohn-f1/", "evaluations": 2, "metric_rows": 2, "charts": 1, "charted_metric_rows": 2, "chart_protocol_ids": [ "genomic-benchmarks-task-human-enhancers-cohn-f1" ], "state": "charts_available", "source_ids": [ "expansion-p3-genomic-benchmarks" ], "source_urls": [ "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10150520/fullTextXML" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "genomic-benchmarks-task-human-enhancers-ensembl-accuracy", "kind": "task", "name": "Genomic Benchmarks HUMAN-ENHANCERS-ENSEMBL-ACCURACY: human_enhancers_ensembl, Accuracy", "status": "source_checked", "url": "/database/task/genomic-benchmarks-task-human-enhancers-ensembl-accuracy/", "evaluations": 2, "metric_rows": 2, "charts": 1, "charted_metric_rows": 2, "chart_protocol_ids": [ "genomic-benchmarks-task-human-enhancers-ensembl-accuracy" ], "state": "charts_available", "source_ids": [ "expansion-p3-genomic-benchmarks" ], "source_urls": [ "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10150520/fullTextXML" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "genomic-benchmarks-task-human-enhancers-ensembl-f1", "kind": "task", "name": "Genomic Benchmarks HUMAN-ENHANCERS-ENSEMBL-F1: human_enhancers_ensembl, F1 score", "status": "source_checked", "url": "/database/task/genomic-benchmarks-task-human-enhancers-ensembl-f1/", "evaluations": 2, "metric_rows": 2, "charts": 1, "charted_metric_rows": 2, "chart_protocol_ids": [ "genomic-benchmarks-task-human-enhancers-ensembl-f1" ], "state": "charts_available", "source_ids": [ "expansion-p3-genomic-benchmarks" ], "source_urls": [ "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10150520/fullTextXML" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "genomic-benchmarks-task-human-ensembl-regulatory-accuracy", "kind": "task", "name": "Genomic Benchmarks HUMAN-ENSEMBL-REGULATORY-ACCURACY: human_ensembl_regulatory, Accuracy", "status": "source_checked", "url": "/database/task/genomic-benchmarks-task-human-ensembl-regulatory-accuracy/", "evaluations": 2, "metric_rows": 2, "charts": 1, "charted_metric_rows": 2, "chart_protocol_ids": [ "genomic-benchmarks-task-human-ensembl-regulatory-accuracy" ], "state": "charts_available", "source_ids": [ "expansion-p3-genomic-benchmarks" ], "source_urls": [ "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10150520/fullTextXML" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "genomic-benchmarks-task-human-ensembl-regulatory-f1", "kind": "task", "name": "Genomic Benchmarks HUMAN-ENSEMBL-REGULATORY-F1: human_ensembl_regulatory, F1 score", "status": "source_checked", "url": "/database/task/genomic-benchmarks-task-human-ensembl-regulatory-f1/", "evaluations": 2, "metric_rows": 2, "charts": 1, "charted_metric_rows": 2, "chart_protocol_ids": [ "genomic-benchmarks-task-human-ensembl-regulatory-f1" ], "state": "charts_available", "source_ids": [ "expansion-p3-genomic-benchmarks" ], "source_urls": [ "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10150520/fullTextXML" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "genomic-benchmarks-task-human-nontata-promoters-accuracy", "kind": "task", "name": "Genomic Benchmarks HUMAN-NONTATA-PROMOTERS-ACCURACY: human_nontata_promoters, Accuracy", "status": "source_checked", "url": "/database/task/genomic-benchmarks-task-human-nontata-promoters-accuracy/", "evaluations": 2, "metric_rows": 2, "charts": 1, "charted_metric_rows": 2, "chart_protocol_ids": [ "genomic-benchmarks-task-human-nontata-promoters-accuracy" ], "state": "charts_available", "source_ids": [ "expansion-p3-genomic-benchmarks" ], "source_urls": [ "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10150520/fullTextXML" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. 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Individual observations remain in the results table." ] }, { "id": "gue-task-transcription-factor-prediction-human-2", "kind": "task", "name": "GUE TRANSCRIPTION-FACTOR-PREDICTION-HUMAN-2: Transcription factor prediction (human), dataset 2", "status": "source_checked", "url": "/database/task/gue-task-transcription-factor-prediction-human-2/", "evaluations": 10, "metric_rows": 10, "charts": 1, "charted_metric_rows": 10, "chart_protocol_ids": [ "gue-task-transcription-factor-prediction-human-2" ], "state": "charts_available", "source_ids": [ "evidence-expansion-gue-49300ace" ], "source_urls": [ "https://arxiv.org/pdf/2306.15006" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "gue-task-transcription-factor-prediction-human-3", "kind": "task", "name": "GUE TRANSCRIPTION-FACTOR-PREDICTION-HUMAN-3: Transcription factor prediction (human), dataset 3", "status": "source_checked", "url": "/database/task/gue-task-transcription-factor-prediction-human-3/", "evaluations": 10, "metric_rows": 10, "charts": 1, "charted_metric_rows": 10, "chart_protocol_ids": [ "gue-task-transcription-factor-prediction-human-3" ], "state": "charts_available", "source_ids": [ "evidence-expansion-gue-49300ace" ], "source_urls": [ "https://arxiv.org/pdf/2306.15006" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "gue-task-transcription-factor-prediction-human-4", "kind": "task", "name": "GUE TRANSCRIPTION-FACTOR-PREDICTION-HUMAN-4: Transcription factor prediction (human), dataset 4", "status": "source_checked", "url": "/database/task/gue-task-transcription-factor-prediction-human-4/", "evaluations": 10, "metric_rows": 10, "charts": 1, "charted_metric_rows": 10, "chart_protocol_ids": [ "gue-task-transcription-factor-prediction-human-4" ], "state": "charts_available", "source_ids": [ "evidence-expansion-gue-49300ace" ], "source_urls": [ "https://arxiv.org/pdf/2306.15006" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "gue-task-transcription-factor-prediction-mouse-0", "kind": "task", "name": "GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-0: Transcription factor prediction (mouse), dataset 0", "status": "source_checked", "url": "/database/task/gue-task-transcription-factor-prediction-mouse-0/", "evaluations": 10, "metric_rows": 10, "charts": 1, "charted_metric_rows": 10, "chart_protocol_ids": [ "gue-task-transcription-factor-prediction-mouse-0" ], "state": "charts_available", "source_ids": [ "evidence-expansion-gue-49300ace" ], "source_urls": [ "https://arxiv.org/pdf/2306.15006" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "gue-task-transcription-factor-prediction-mouse-1", "kind": "task", "name": "GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-1: Transcription factor prediction (mouse), dataset 1", "status": "source_checked", "url": "/database/task/gue-task-transcription-factor-prediction-mouse-1/", "evaluations": 10, "metric_rows": 10, "charts": 1, "charted_metric_rows": 10, "chart_protocol_ids": [ "gue-task-transcription-factor-prediction-mouse-1" ], "state": "charts_available", "source_ids": [ "evidence-expansion-gue-49300ace" ], "source_urls": [ "https://arxiv.org/pdf/2306.15006" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "gue-task-transcription-factor-prediction-mouse-2", "kind": "task", "name": "GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-2: Transcription factor prediction (mouse), dataset 2", "status": "source_checked", "url": "/database/task/gue-task-transcription-factor-prediction-mouse-2/", "evaluations": 10, "metric_rows": 10, "charts": 1, "charted_metric_rows": 10, "chart_protocol_ids": [ "gue-task-transcription-factor-prediction-mouse-2" ], "state": "charts_available", "source_ids": [ "evidence-expansion-gue-49300ace" ], "source_urls": [ "https://arxiv.org/pdf/2306.15006" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "gue-task-transcription-factor-prediction-mouse-3", "kind": "task", "name": "GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-3: Transcription factor prediction (mouse), dataset 3", "status": "source_checked", "url": "/database/task/gue-task-transcription-factor-prediction-mouse-3/", "evaluations": 10, "metric_rows": 10, "charts": 1, "charted_metric_rows": 10, "chart_protocol_ids": [ "gue-task-transcription-factor-prediction-mouse-3" ], "state": "charts_available", "source_ids": [ "evidence-expansion-gue-49300ace" ], "source_urls": [ "https://arxiv.org/pdf/2306.15006" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "gue-task-transcription-factor-prediction-mouse-4", "kind": "task", "name": "GUE TRANSCRIPTION-FACTOR-PREDICTION-MOUSE-4: Transcription factor prediction (mouse), dataset 4", "status": "source_checked", "url": "/database/task/gue-task-transcription-factor-prediction-mouse-4/", "evaluations": 10, "metric_rows": 10, "charts": 1, "charted_metric_rows": 10, "chart_protocol_ids": [ "gue-task-transcription-factor-prediction-mouse-4" ], "state": "charts_available", "source_ids": [ "evidence-expansion-gue-49300ace" ], "source_urls": [ "https://arxiv.org/pdf/2306.15006" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "catalog-task-heldout-clade", "kind": "task", "name": "Held-out-clade classification", "status": "discovered", "url": "/database/task/catalog-task-heldout-clade/", "evaluations": 0, "metric_rows": 0, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_not_yet_collected", "source_ids": [ "catalog-source-prokbert", "catalog-source-metagene-1", "catalog-source-evo-2", "catalog-source-kraken2", "expansion-p3-barcodebert-2026", "barcodebert-2026" ], "source_urls": [ "https://github.com/nbrg-ppcu/prokbert", "https://huggingface.co/metagene-ai/METAGENE-1", "https://github.com/ArcInstitute/evo2", "https://github.com/DerrickWood/kraken2", "https://pmc.ncbi.nlm.nih.gov/articles/PMC13008329/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC13008329/" ], "research_status": "broad_task_primary_protocol_linked", "research_review_date": "2026-09-17", "gaps": [ "Table does not give uncertainty for each genus accuracy; BLAST is an alignment reference, not a pretrained encoder." ] }, { "id": "hest-task-ccrcc", "kind": "task", "name": "HEST-Benchmark CCRCC: Gene expression prediction from histology, Clear cell renal cell carcinoma", "status": "source_checked", "url": "/database/task/hest-task-ccrcc/", "evaluations": 10, "metric_rows": 10, "charts": 1, "charted_metric_rows": 10, "chart_protocol_ids": [ "hest-task-ccrcc" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-hest-cached-636099a73dee" ], "source_urls": [ "https://arxiv.org/pdf/2406.16192v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "hest-task-coad", "kind": "task", "name": "HEST-Benchmark COAD: Gene expression prediction from histology, Colon adenocarcinoma", "status": "source_checked", "url": "/database/task/hest-task-coad/", "evaluations": 10, "metric_rows": 10, "charts": 1, "charted_metric_rows": 10, "chart_protocol_ids": [ "hest-task-coad" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-hest-cached-636099a73dee" ], "source_urls": [ "https://arxiv.org/pdf/2406.16192v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "hest-task-hcc", "kind": "task", "name": "HEST-Benchmark HCC: Gene expression prediction from histology, Hepatocellular carcinoma", "status": "source_checked", "url": "/database/task/hest-task-hcc/", "evaluations": 10, "metric_rows": 10, "charts": 1, "charted_metric_rows": 10, "chart_protocol_ids": [ "hest-task-hcc" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-hest-cached-636099a73dee" ], "source_urls": [ "https://arxiv.org/pdf/2406.16192v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "hest-task-idc", "kind": "task", "name": "HEST-Benchmark IDC: Gene expression prediction from histology, Invasive ductal carcinoma", "status": "source_checked", "url": "/database/task/hest-task-idc/", "evaluations": 10, "metric_rows": 10, "charts": 1, "charted_metric_rows": 10, "chart_protocol_ids": [ "hest-task-idc" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-hest-cached-636099a73dee" ], "source_urls": [ "https://arxiv.org/pdf/2406.16192v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "hest-task-lung", "kind": "task", "name": "HEST-Benchmark LUNG: Gene expression prediction from histology, Lung", "status": "source_checked", "url": "/database/task/hest-task-lung/", "evaluations": 10, "metric_rows": 10, "charts": 1, "charted_metric_rows": 10, "chart_protocol_ids": [ "hest-task-lung" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-hest-cached-636099a73dee" ], "source_urls": [ "https://arxiv.org/pdf/2406.16192v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "hest-task-lymph-idc", "kind": "task", "name": "HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma", "status": "source_checked", "url": "/database/task/hest-task-lymph-idc/", "evaluations": 10, "metric_rows": 10, "charts": 1, "charted_metric_rows": 10, "chart_protocol_ids": [ "hest-task-lymph-idc" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-hest-cached-636099a73dee" ], "source_urls": [ "https://arxiv.org/pdf/2406.16192v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "hest-task-paad", "kind": "task", "name": "HEST-Benchmark PAAD: Gene expression prediction from histology, Pancreatic adenocarcinoma", "status": "source_checked", "url": "/database/task/hest-task-paad/", "evaluations": 10, "metric_rows": 10, "charts": 1, "charted_metric_rows": 10, "chart_protocol_ids": [ "hest-task-paad" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-hest-cached-636099a73dee" ], "source_urls": [ "https://arxiv.org/pdf/2406.16192v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "hest-task-prad", "kind": "task", "name": "HEST-Benchmark PRAD: Gene expression prediction from histology, Prostate adenocarcinoma", "status": "source_checked", "url": "/database/task/hest-task-prad/", "evaluations": 10, "metric_rows": 10, "charts": 1, "charted_metric_rows": 10, "chart_protocol_ids": [ "hest-task-prad" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-hest-cached-636099a73dee" ], "source_urls": [ "https://arxiv.org/pdf/2406.16192v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "hest-task-read", "kind": "task", "name": "HEST-Benchmark READ: Gene expression prediction from histology, Rectum adenocarcinoma", "status": "source_checked", "url": "/database/task/hest-task-read/", "evaluations": 10, "metric_rows": 10, "charts": 1, "charted_metric_rows": 10, "chart_protocol_ids": [ "hest-task-read" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-hest-cached-636099a73dee" ], "source_urls": [ "https://arxiv.org/pdf/2406.16192v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "hest-task-skcm", "kind": "task", "name": "HEST-Benchmark SKCM: Gene expression prediction from histology, Skin cutaneous melanoma", "status": "source_checked", "url": "/database/task/hest-task-skcm/", "evaluations": 10, "metric_rows": 10, "charts": 1, "charted_metric_rows": 10, "chart_protocol_ids": [ "hest-task-skcm" ], "state": "charts_available", "source_ids": [ "evidence-expansion-p2-hest-cached-636099a73dee" ], "source_urls": [ "https://arxiv.org/pdf/2406.16192v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "reported-task-f4b1c9373f0929", "kind": "task", "name": "Hierarchical metagenomic taxonomy classification", "status": "needs_review", "url": "/database/task/reported-task-f4b1c9373f0929/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "icctax-2025", "expansion-p3-icctax-2025" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12619997/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12619997/" ], "research_status": "primary_comparison_table_screened", "research_review_date": "2026-09-17", "gaps": [ "MetaPhlAn4 uses its official prebuilt database, unlike the common training database; preserve the asterisk.", "CAT and MetaPhlAn4 do not supply probabilities, so AveP is inapplicable, not zero.", "Bootstrap intervals exist in supplemental figures; main-table values lack printed intervals." ] }, { "id": "reported-task-988ff78f86471e", "kind": "task", "name": "Human 5mC detection", "status": "needs_review", "url": "/database/task/reported-task-988ff78f86471e/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "dna-foundation-models-2025", "evidence-expansion-dna-foundation-models-2025-5d8ca9bc" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12663285/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12663285/" ], "research_status": "primary_comparison_tables_located", "research_review_date": "2026-09-17", "gaps": [ "complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.", "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "reported-task-9f62e739c6371e", "kind": "task", "name": "human core-promoter classification", "status": "needs_review", "url": "/database/task/reported-task-9f62e739c6371e/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "eden-genomic-classification-2026", "evidence-expansion-eden-genomic-classification-2026-38a6e26b" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12879454/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12879454/" ], "research_status": "primary_comparison_tables_located", "research_review_date": "2026-09-17", "gaps": [ "complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.", "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "reported-task-6e54c7452b2b81", "kind": "task", "name": "human protein-protein interaction prediction", "status": "needs_review", "url": "/database/task/reported-task-6e54c7452b2b81/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "mulan-2025", "evidence-expansion-p2-mulan-2025-771a9a26ebda" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12452268/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12452268/fullTextXML" ], "research_status": "source_found_structured_extraction_pending", "research_review_date": "2026-09-17", "gaps": [ "Complete raw table acquired. HumanPPI AUC column must be extracted separately from localization, thermostability,fluorescence andGO. Different model sizes/representation inputs remain distinct. Structured extraction pending." ] }, { "id": "reported-task-82fc7843f07324", "kind": "task", "name": "human RNA 2-prime-O-methylation site prediction", "status": "needs_review", "url": "/database/task/reported-task-82fc7843f07324/", "evaluations": 12, "metric_rows": 84, "charts": 14, "charted_metric_rows": 84, "chart_protocol_ids": [ "paper-protocol-1e891689a18fea3b65", "paper-protocol-d933438afda70a21ef" ], "state": "charts_available", "source_ids": [ "2ome-lm-2025", "evidence-expansion-2ome-lm-2025-54fe4db6" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12342186/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12342186/" ], "research_status": "complete_tables_extracted", "research_review_date": "2026-09-17", "gaps": [ "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "reported-task-031186b57c62de", "kind": "task", "name": "Human thymus cell-type classification", "status": "needs_review", "url": "/database/task/reported-task-031186b57c62de/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "mouse-geneformer-2025", "expansion-p3-mouse-geneformer-2025" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC11964219/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC11964219/" ], "research_status": "primary_comparison_table_screened", "research_review_date": "2026-09-17", "gaps": [ "Only the thymus row belongs to the assigned benchmark; cortex and breast must be separate protocols.", "The authors' Euclidean nonidentity check is not proof that all leakage is absent; source wording must not become an independently established guarantee.", "No replicate uncertainty in Table 4." ] }, { "id": "reported-task-53506fe386e4a1", "kind": "task", "name": "human-versus-viral protein classification", "status": "needs_review", "url": "/database/task/reported-task-53506fe386e4a1/", "evaluations": 8, "metric_rows": 32, "charts": 4, "charted_metric_rows": 32, "chart_protocol_ids": [ "paper-protocol-1352834b9391c1dacb" ], "state": "charts_available", "source_ids": [ "viral-immune-mimicry-2025", "part2-viral-immune-mimicry-2025" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12474240/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12474240/fullTextXML" ], "research_status": "complete_comparison_tables_extracted_pending_publication_review", "research_review_date": "2026-09-17", "gaps": [ "Independent batch review before import; 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no new numeric row is published from this audit alone.", "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "reported-task-ff2dec63c5a3dd", "kind": "task", "name": "Lipid–protein binding pose", "status": "needs_review", "url": "/database/task/reported-task-ff2dec63c5a3dd/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "lipp-2026", "evidence-expansion-p2-lipp-2026-6ff34f2f709a" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC13292216/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13292216/fullTextXML" ], "research_status": "source_found_structured_extraction_pending", "research_review_date": "2026-09-17", "gaps": [ "Complete raw tables acquired. 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Record ten as reported, with discrepancy, not an inferred tenth seed.", "Tables 5–6 uncertainties are 95% confidence intervals, not standard deviations.", "Task/subtask pooling and transformed aggregate rankings must not be conflated with printed raw metrics." ] }, { "id": "reported-task-4420dcdfe8338d", "kind": "task", "name": "metagenomic genus classification", "status": "needs_review", "url": "/database/task/reported-task-4420dcdfe8338d/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "pc-mer-2024", "evidence-expansion-p2-pc-mer-2024-0b0a225fa6f5" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC11293629/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11293629/fullTextXML" ], "research_status": "source_found_structured_extraction_pending", "research_review_date": "2026-09-17", "gaps": [ "Complete raw table acquired. 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Reference database state required before chart groups. Structured extraction pending." ] }, { "id": "catalog-task-mfass-splice", "kind": "task", "name": "MFASS splice-variant prioritisation", "status": "discovered", "url": "/database/task/catalog-task-mfass-splice/", "evaluations": 9, "metric_rows": 31, "charts": 4, "charted_metric_rows": 16, "chart_protocol_ids": [ "rewire-mfass-matched-v1-protocol" ], "state": "charts_available", "source_ids": [ "catalog-source-dnabert-2", "catalog-source-nt-v2", "catalog-source-spliceai", "catalog-source-pangolin", "evidence-expansion-p2-mfass-original-noartifact-2", "evidence-expansion-p2-mfass-primary-bibliographic-noartifact-2", "rewire-mfass-v2-source", "evidence-benchmark-mfass-pinned-readme", "profile-protocol-mfass-results-compare-baseline-v2-vs-spliceai-json-77900982", "profile-protocol-mfass-results-compare-baseline-v2-vs-pangolin-maskfalse-json-fd938e14", "profile-protocol-mfass-results-compare-baseline-v2-vs-dnabert2-json-52216e00", "profile-protocol-mfass-metrics-py-4030374e" ], "source_urls": [ "https://huggingface.co/zhihan1996/DNABERT-2-117M", "https://huggingface.co/InstaDeepAI/nucleotide-transformer-v2-50m-multi-species", "https://github.com/Illumina/SpliceAI", "https://github.com/tkzeng/Pangolin", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC6599603/fullTextXML", "https://pmc.ncbi.nlm.nih.gov/articles/PMC6599603/", "https://github.com/timini/rewire-benchmarks/tree/bee9133b83f3aedaf2bbb9013f1875515845607e", "https://github.com/timini/rewire-benchmarks/blob/bee9133b83f3aedaf2bbb9013f1875515845607e/benchmarks/mfass/README.md", "https://raw.githubusercontent.com/rewire-bio/rewire-benchmarks/bee9133b83f3aedaf2bbb9013f1875515845607e/benchmarks/mfass/results/compare-baseline-v2-vs-spliceai.json", "https://raw.githubusercontent.com/rewire-bio/rewire-benchmarks/bee9133b83f3aedaf2bbb9013f1875515845607e/benchmarks/mfass/results/compare-baseline-v2-vs-pangolin-maskFalse.json", "https://raw.githubusercontent.com/rewire-bio/rewire-benchmarks/bee9133b83f3aedaf2bbb9013f1875515845607e/benchmarks/mfass/results/compare-baseline-v2-vs-dnabert2.json", "https://raw.githubusercontent.com/rewire-bio/rewire-benchmarks/bee9133b83f3aedaf2bbb9013f1875515845607e/packages/rewirebench/src/rewirebench/metrics.py" ], "research_status": "broad_task_primary_raw_retrieval_blocked_existing_corrected_run_retained", "research_review_date": "2026-09-17", "gaps": [ "Primary browser text accessible but rawXML endpoint 500, PMC HTMLreCAPTCHA and mirror returned 0 bytes. 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no new numeric row is published from this audit alone.", "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "reported-task-8406b6aabfb8c0", "kind": "task", "name": "Mock-community MAG taxonomy classification", "status": "needs_review", "url": "/database/task/reported-task-8406b6aabfb8c0/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "kmetashot-2025", "expansion-p3-kmetashot-2025" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC11695915/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC11695915/" ], "research_status": "primary_comparison_table_screened", "research_review_date": "2026-09-17", "gaps": [ "Do not pool assemblies, ranks or raw/corrected taxonomic labels.", "Table entries such as '9 + 33' and '8 + 35' are printed decompositions, not unambiguous single numerical observations.", "Total MAGs and metric confusion-matrix denominators differ; 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Individual observations remain in the results table." ] }, { "id": "mrnabench-task-mrl-hl-pair", "kind": "task", "name": "mRNABench MRL-HL-PAIR: Paired mean ribosome load and half life", "status": "source_checked", "url": "/database/task/mrnabench-task-mrl-hl-pair/", "evaluations": 21, "metric_rows": 21, "charts": 1, "charted_metric_rows": 21, "chart_protocol_ids": [ "mrnabench-task-mrl-hl-pair" ], "state": "charts_available", "source_ids": [ "expansion-p3-mrnabench-2025" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12265608/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "mrnabench-task-mrl-mpra", "kind": "task", "name": "mRNABench MRL-MPRA: Mean ribosome load on an MPRA library", "status": "source_checked", "url": "/database/task/mrnabench-task-mrl-mpra/", "evaluations": 21, "metric_rows": 21, "charts": 1, "charted_metric_rows": 21, "chart_protocol_ids": [ "mrnabench-task-mrl-mpra" ], "state": "charts_available", "source_ids": [ "expansion-p3-mrnabench-2025" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12265608/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "mrnabench-task-mrl", "kind": "task", "name": "mRNABench MRL: Mean ribosome load", "status": "source_checked", "url": "/database/task/mrnabench-task-mrl/", "evaluations": 21, "metric_rows": 21, "charts": 1, "charted_metric_rows": 21, "chart_protocol_ids": [ "mrnabench-task-mrl" ], "state": "charts_available", "source_ids": [ "expansion-p3-mrnabench-2025" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12265608/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "mrnabench-task-mrna-loc-lr", "kind": "task", "name": "mRNABench MRNA-LOC-LR: mRNA localisation, long range", "status": "source_checked", "url": "/database/task/mrnabench-task-mrna-loc-lr/", "evaluations": 21, "metric_rows": 21, "charts": 1, "charted_metric_rows": 21, "chart_protocol_ids": [ "mrnabench-task-mrna-loc-lr" ], "state": "charts_available", "source_ids": [ "expansion-p3-mrnabench-2025" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12265608/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "mrnabench-task-mrna-loc-sr", "kind": "task", "name": "mRNABench MRNA-LOC-SR: mRNA localisation, short range", "status": "source_checked", "url": "/database/task/mrnabench-task-mrna-loc-sr/", "evaluations": 21, "metric_rows": 21, "charts": 1, "charted_metric_rows": 21, "chart_protocol_ids": [ "mrnabench-task-mrna-loc-sr" ], "state": "charts_available", "source_ids": [ "expansion-p3-mrnabench-2025" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12265608/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "mrnabench-task-prot-loc", "kind": "task", "name": "mRNABench PROT-LOC: Protein localisation", "status": "source_checked", "url": "/database/task/mrnabench-task-prot-loc/", "evaluations": 21, "metric_rows": 21, "charts": 1, "charted_metric_rows": 21, "chart_protocol_ids": [ "mrnabench-task-prot-loc" ], "state": "charts_available", "source_ids": [ "expansion-p3-mrnabench-2025" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12265608/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "mrnabench-task-vep", "kind": "task", "name": "mRNABench VEP: Variant effect prediction", "status": "source_checked", "url": "/database/task/mrnabench-task-vep/", "evaluations": 21, "metric_rows": 21, "charts": 1, "charted_metric_rows": 21, "chart_protocol_ids": [ "mrnabench-task-vep" ], "state": "charts_available", "source_ids": [ "expansion-p3-mrnabench-2025" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12265608/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "reported-task-a1151e386a3d3f", "kind": "task", "name": "Multi-species prokaryotic promoter detection", "status": "needs_review", "url": "/database/task/reported-task-a1151e386a3d3f/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "ipromp-2025", "expansion-p3-ipromp-2025" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12516880/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12516880/" ], "research_status": "primary_comparison_table_screened", "research_review_date": "2026-09-17", "gaps": [ "iPro-MP's first four scores duplicate across Tables 1–2; one result with two source occurrences.", "Species-averaged accuracy/AUROC/AUPRC/MCC differ from pooled sample scores; retain source aggregation.", "Runtime is seconds, lower-is-better, and hardware-dependent." ] }, { "id": "reported-task-00e594df6a182d", "kind": "task", "name": "Mutated RBD binding prediction", "status": "needs_review", "url": "/database/task/reported-task-00e594df6a182d/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "prime-2026", "evidence-expansion-prime-2026-f6aac4c2" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC13425921/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC13425921/" ], "research_status": "primary_comparison_tables_located", "research_review_date": "2026-09-17", "gaps": [ "complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.", "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "nabench-task-ccv-corr-aptamer", "kind": "task", "name": "NABench CCV-CORR-APTAMER: Fitness prediction on aptamer assays, supervised, contiguous cross validation", "status": "source_checked", "url": "/database/task/nabench-task-ccv-corr-aptamer/", "evaluations": 25, "metric_rows": 25, "charts": 1, "charted_metric_rows": 25, "chart_protocol_ids": [ "nabench-task-ccv-corr-aptamer" ], "state": "charts_available", "source_ids": [ "evidence-expansion-nabench-fefd48d5" ], "source_urls": [ "https://arxiv.org/html/2511.02888v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "nabench-task-ccv-corr-enhancer", "kind": "task", "name": "NABench CCV-CORR-ENHANCER: Fitness prediction on enhancer assays, supervised, contiguous cross validation", "status": "source_checked", "url": "/database/task/nabench-task-ccv-corr-enhancer/", "evaluations": 25, "metric_rows": 25, "charts": 1, "charted_metric_rows": 25, "chart_protocol_ids": [ "nabench-task-ccv-corr-enhancer" ], "state": "charts_available", "source_ids": [ "evidence-expansion-nabench-fefd48d5" ], "source_urls": [ "https://arxiv.org/html/2511.02888v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "nabench-task-ccv-corr-mrna", "kind": "task", "name": "NABench CCV-CORR-MRNA: Fitness prediction on mRNA assays, supervised, contiguous cross validation", "status": "source_checked", "url": "/database/task/nabench-task-ccv-corr-mrna/", "evaluations": 25, "metric_rows": 25, "charts": 1, "charted_metric_rows": 25, "chart_protocol_ids": [ "nabench-task-ccv-corr-mrna" ], "state": "charts_available", "source_ids": [ "evidence-expansion-nabench-fefd48d5" ], "source_urls": [ "https://arxiv.org/html/2511.02888v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "nabench-task-ccv-corr-promoter", "kind": "task", "name": "NABench CCV-CORR-PROMOTER: Fitness prediction on promoter assays, supervised, contiguous cross validation", "status": "source_checked", "url": "/database/task/nabench-task-ccv-corr-promoter/", "evaluations": 23, "metric_rows": 23, "charts": 1, "charted_metric_rows": 23, "chart_protocol_ids": [ "nabench-task-ccv-corr-promoter" ], "state": "charts_available", "source_ids": [ "evidence-expansion-nabench-fefd48d5" ], "source_urls": [ "https://arxiv.org/html/2511.02888v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "nabench-task-ccv-corr-ribozyme", "kind": "task", "name": "NABench CCV-CORR-RIBOZYME: Fitness prediction on ribozyme assays, supervised, contiguous cross validation", "status": "source_checked", "url": "/database/task/nabench-task-ccv-corr-ribozyme/", "evaluations": 25, "metric_rows": 25, "charts": 1, "charted_metric_rows": 25, "chart_protocol_ids": [ "nabench-task-ccv-corr-ribozyme" ], "state": "charts_available", "source_ids": [ "evidence-expansion-nabench-fefd48d5" ], "source_urls": [ "https://arxiv.org/html/2511.02888v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "nabench-task-ccv-corr-trna", "kind": "task", "name": "NABench CCV-CORR-TRNA: Fitness prediction on tRNA assays, supervised, contiguous cross validation", "status": "source_checked", "url": "/database/task/nabench-task-ccv-corr-trna/", "evaluations": 24, "metric_rows": 24, "charts": 1, "charted_metric_rows": 24, "chart_protocol_ids": [ "nabench-task-ccv-corr-trna" ], "state": "charts_available", "source_ids": [ "evidence-expansion-nabench-fefd48d5" ], "source_urls": [ "https://arxiv.org/html/2511.02888v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "nabench-task-dms-ccv", "kind": "task", "name": "NABench DMS-CCV: Overall fitness prediction on NABench deep mutational scanning assays, Contiguous cross validation Spearman ρ", "status": "source_checked", "url": "/database/task/nabench-task-dms-ccv/", "evaluations": 25, "metric_rows": 25, "charts": 1, "charted_metric_rows": 25, "chart_protocol_ids": [ "nabench-task-dms-ccv" ], "state": "charts_available", "source_ids": [ "evidence-expansion-nabench-fefd48d5" ], "source_urls": [ "https://arxiv.org/html/2511.02888v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "nabench-task-dms-fs", "kind": "task", "name": "NABench DMS-FS: Overall fitness prediction on NABench deep mutational scanning assays, Few-shot Spearman ρ", "status": "source_checked", "url": "/database/task/nabench-task-dms-fs/", "evaluations": 25, "metric_rows": 25, "charts": 1, "charted_metric_rows": 25, "chart_protocol_ids": [ "nabench-task-dms-fs" ], "state": "charts_available", "source_ids": [ "evidence-expansion-nabench-fefd48d5" ], "source_urls": [ "https://arxiv.org/html/2511.02888v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "nabench-task-dms-rcv", "kind": "task", "name": "NABench DMS-RCV: Overall fitness prediction on NABench deep mutational scanning assays, Random cross validation Spearman ρ", "status": "source_checked", "url": "/database/task/nabench-task-dms-rcv/", "evaluations": 25, "metric_rows": 25, "charts": 1, "charted_metric_rows": 25, "chart_protocol_ids": [ "nabench-task-dms-rcv" ], "state": "charts_available", "source_ids": [ "evidence-expansion-nabench-fefd48d5" ], "source_urls": [ "https://arxiv.org/html/2511.02888v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "nabench-task-dms-zs-auc", "kind": "task", "name": "NABench DMS-ZS-AUC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot AUC", "status": "source_checked", "url": "/database/task/nabench-task-dms-zs-auc/", "evaluations": 25, "metric_rows": 25, "charts": 1, "charted_metric_rows": 25, "chart_protocol_ids": [ "nabench-task-dms-zs-auc" ], "state": "charts_available", "source_ids": [ "evidence-expansion-nabench-fefd48d5" ], "source_urls": [ "https://arxiv.org/html/2511.02888v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "nabench-task-dms-zs-corr", "kind": "task", "name": "NABench DMS-ZS-CORR: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot Spearman ρ", "status": "source_checked", "url": "/database/task/nabench-task-dms-zs-corr/", "evaluations": 25, "metric_rows": 25, "charts": 1, "charted_metric_rows": 25, "chart_protocol_ids": [ "nabench-task-dms-zs-corr" ], "state": "charts_available", "source_ids": [ "evidence-expansion-nabench-fefd48d5" ], "source_urls": [ "https://arxiv.org/html/2511.02888v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "nabench-task-dms-zs-mcc", "kind": "task", "name": "NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC", "status": "source_checked", "url": "/database/task/nabench-task-dms-zs-mcc/", "evaluations": 25, "metric_rows": 25, "charts": 1, "charted_metric_rows": 25, "chart_protocol_ids": [ "nabench-task-dms-zs-mcc" ], "state": "charts_available", "source_ids": [ "evidence-expansion-nabench-fefd48d5" ], "source_urls": [ "https://arxiv.org/html/2511.02888v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "nabench-task-dms-zs-ndcg", "kind": "task", "name": "NABench DMS-ZS-NDCG: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot NDCG", "status": "source_checked", "url": "/database/task/nabench-task-dms-zs-ndcg/", "evaluations": 25, "metric_rows": 25, "charts": 1, "charted_metric_rows": 25, "chart_protocol_ids": [ "nabench-task-dms-zs-ndcg" ], "state": "charts_available", "source_ids": [ "evidence-expansion-nabench-fefd48d5" ], "source_urls": [ "https://arxiv.org/html/2511.02888v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "nabench-task-fs-corr-aptamer", "kind": "task", "name": "NABench FS-CORR-APTAMER: Fitness prediction on aptamer assays, few-shot", "status": "source_checked", "url": "/database/task/nabench-task-fs-corr-aptamer/", "evaluations": 26, "metric_rows": 26, "charts": 1, "charted_metric_rows": 26, "chart_protocol_ids": [ "nabench-task-fs-corr-aptamer" ], "state": "charts_available", "source_ids": [ "evidence-expansion-nabench-fefd48d5" ], "source_urls": [ "https://arxiv.org/html/2511.02888v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "nabench-task-fs-corr-enhancer", "kind": "task", "name": "NABench FS-CORR-ENHANCER: Fitness prediction on enhancer assays, few-shot", "status": "source_checked", "url": "/database/task/nabench-task-fs-corr-enhancer/", "evaluations": 26, "metric_rows": 26, "charts": 1, "charted_metric_rows": 26, "chart_protocol_ids": [ "nabench-task-fs-corr-enhancer" ], "state": "charts_available", "source_ids": [ "evidence-expansion-nabench-fefd48d5" ], "source_urls": [ "https://arxiv.org/html/2511.02888v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "nabench-task-fs-corr-mrna", "kind": "task", "name": "NABench FS-CORR-MRNA: Fitness prediction on mRNA assays, few-shot", "status": "source_checked", "url": "/database/task/nabench-task-fs-corr-mrna/", "evaluations": 26, "metric_rows": 26, "charts": 1, "charted_metric_rows": 26, "chart_protocol_ids": [ "nabench-task-fs-corr-mrna" ], "state": "charts_available", "source_ids": [ "evidence-expansion-nabench-fefd48d5" ], "source_urls": [ "https://arxiv.org/html/2511.02888v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "nabench-task-fs-corr-promoter", "kind": "task", "name": "NABench FS-CORR-PROMOTER: Fitness prediction on promoter assays, few-shot", "status": "source_checked", "url": "/database/task/nabench-task-fs-corr-promoter/", "evaluations": 26, "metric_rows": 26, "charts": 1, "charted_metric_rows": 26, "chart_protocol_ids": [ "nabench-task-fs-corr-promoter" ], "state": "charts_available", "source_ids": [ "evidence-expansion-nabench-fefd48d5" ], "source_urls": [ "https://arxiv.org/html/2511.02888v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "nabench-task-fs-corr-ribozyme", "kind": "task", "name": "NABench FS-CORR-RIBOZYME: Fitness prediction on ribozyme assays, few-shot", "status": "source_checked", "url": "/database/task/nabench-task-fs-corr-ribozyme/", "evaluations": 26, "metric_rows": 26, "charts": 1, "charted_metric_rows": 26, "chart_protocol_ids": [ "nabench-task-fs-corr-ribozyme" ], "state": "charts_available", "source_ids": [ "evidence-expansion-nabench-fefd48d5" ], "source_urls": [ "https://arxiv.org/html/2511.02888v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "nabench-task-fs-corr-trna", "kind": "task", "name": "NABench FS-CORR-TRNA: Fitness prediction on tRNA assays, few-shot", "status": "source_checked", "url": "/database/task/nabench-task-fs-corr-trna/", "evaluations": 25, "metric_rows": 25, "charts": 1, "charted_metric_rows": 25, "chart_protocol_ids": [ "nabench-task-fs-corr-trna" ], "state": "charts_available", "source_ids": [ "evidence-expansion-nabench-fefd48d5" ], "source_urls": [ "https://arxiv.org/html/2511.02888v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "nabench-task-rcv-corr-aptamer", "kind": "task", "name": "NABench RCV-CORR-APTAMER: Fitness prediction on aptamer assays, supervised, random cross validation", "status": "source_checked", "url": "/database/task/nabench-task-rcv-corr-aptamer/", "evaluations": 26, "metric_rows": 26, "charts": 1, "charted_metric_rows": 26, "chart_protocol_ids": [ "nabench-task-rcv-corr-aptamer" ], "state": "charts_available", "source_ids": [ "evidence-expansion-nabench-fefd48d5" ], "source_urls": [ "https://arxiv.org/html/2511.02888v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "nabench-task-rcv-corr-enhancer", "kind": "task", "name": "NABench RCV-CORR-ENHANCER: Fitness prediction on enhancer assays, supervised, random cross validation", "status": "source_checked", "url": "/database/task/nabench-task-rcv-corr-enhancer/", "evaluations": 26, "metric_rows": 26, "charts": 1, "charted_metric_rows": 26, "chart_protocol_ids": [ "nabench-task-rcv-corr-enhancer" ], "state": "charts_available", "source_ids": [ "evidence-expansion-nabench-fefd48d5" ], "source_urls": [ "https://arxiv.org/html/2511.02888v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "nabench-task-rcv-corr-mrna", "kind": "task", "name": "NABench RCV-CORR-MRNA: Fitness prediction on mRNA assays, supervised, random cross validation", "status": "source_checked", "url": "/database/task/nabench-task-rcv-corr-mrna/", "evaluations": 26, "metric_rows": 26, "charts": 1, "charted_metric_rows": 26, "chart_protocol_ids": [ "nabench-task-rcv-corr-mrna" ], "state": "charts_available", "source_ids": [ "evidence-expansion-nabench-fefd48d5" ], "source_urls": [ "https://arxiv.org/html/2511.02888v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "nabench-task-rcv-corr-promoter", "kind": "task", "name": "NABench RCV-CORR-PROMOTER: Fitness prediction on promoter assays, supervised, random cross validation", "status": "source_checked", "url": "/database/task/nabench-task-rcv-corr-promoter/", "evaluations": 26, "metric_rows": 26, "charts": 1, "charted_metric_rows": 26, "chart_protocol_ids": [ "nabench-task-rcv-corr-promoter" ], "state": "charts_available", "source_ids": [ "evidence-expansion-nabench-fefd48d5" ], "source_urls": [ "https://arxiv.org/html/2511.02888v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. 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Individual observations remain in the results table." ] }, { "id": "open-problems-task-zebrafish-labs-accuracy", "kind": "task", "name": "Open Problems label projection ZEBRAFISH-LABS-ACCURACY: Label projection on Zebrafish (by laboratory), Accuracy", "status": "source_checked", "url": "/database/task/open-problems-task-zebrafish-labs-accuracy/", "evaluations": 16, "metric_rows": 16, "charts": 1, "charted_metric_rows": 16, "chart_protocol_ids": [ "open-problems-task-zebrafish-labs-accuracy" ], "state": "charts_available", "source_ids": [ "expansion-p3-open-problems" ], "source_urls": [ "https://www.openproblems.bio/benchmarks/label_projection/v1.0.0/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. 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Individual observations remain in the results table." ] }, { "id": "open-problems-task-zebrafish-random-f1-macro", "kind": "task", "name": "Open Problems label projection ZEBRAFISH-RANDOM-F1-MACRO: Label projection on Zebrafish (random split), Macro F1 score", "status": "source_checked", "url": "/database/task/open-problems-task-zebrafish-random-f1-macro/", "evaluations": 16, "metric_rows": 16, "charts": 1, "charted_metric_rows": 16, "chart_protocol_ids": [ "open-problems-task-zebrafish-random-f1-macro" ], "state": "charts_available", "source_ids": [ "expansion-p3-open-problems" ], "source_urls": [ "https://www.openproblems.bio/benchmarks/label_projection/v1.0.0/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "open-problems-task-zebrafish-random-f1", "kind": "task", "name": "Open Problems label projection ZEBRAFISH-RANDOM-F1: Label projection on Zebrafish (random split), F1 score", "status": "source_checked", "url": "/database/task/open-problems-task-zebrafish-random-f1/", "evaluations": 16, "metric_rows": 16, "charts": 1, "charted_metric_rows": 16, "chart_protocol_ids": [ "open-problems-task-zebrafish-random-f1" ], "state": "charts_available", "source_ids": [ "expansion-p3-open-problems" ], "source_urls": [ "https://www.openproblems.bio/benchmarks/label_projection/v1.0.0/" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "reported-task-d3fd502fdc2b38", "kind": "task", "name": "pathogen detection", "status": "needs_review", "url": "/database/task/reported-task-d3fd502fdc2b38/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "metagenomic-pathogens-2025", "expansion-p3-metagenomic-pathogens-2025" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12493982/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12493982/" ], "research_status": "source_concern_comparison_blocked", "research_review_date": "2026-09-17", "gaps": [ "Comparison blocked: Section 4.3 lacks exact sample/split manifest and reference-label construction.", "Section 4.2 five-fold procedure concerns other datasets and cannot be assigned to Table 3.", "Do not claim the genomic experiment is absent: Section 4.3 explicitly describes it." ] }, { "id": "reported-task-b46b7b839bff93", "kind": "task", "name": "PBMC cell-type classification", "status": "needs_review", "url": "/database/task/reported-task-b46b7b839bff93/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "scalr-2025", "evidence-expansion-p2-scalr-2025-829afab6a4e3" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12121358/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12121358/fullTextXML" ], "research_status": "source_found_structured_extraction_pending", "research_review_date": "2026-09-17", "gaps": [ "Complete raw table acquired. 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Individual observations remain in the results table." ] }, { "id": "perturbench-task-ct-rmse", "kind": "task", "name": "PerturBench CT-RMSE: covariate transfer on Srivatsan20, RMSE of the mean", "status": "source_checked", "url": "/database/task/perturbench-task-ct-rmse/", "evaluations": 10, "metric_rows": 10, "charts": 1, "charted_metric_rows": 10, "chart_protocol_ids": [ "perturbench-task-ct-rmse" ], "state": "charts_available", "source_ids": [ "evidence-expansion-perturbench-5c480456" ], "source_urls": [ "https://arxiv.org/html/2408.10609v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "pfmbench-task-anti-res", "kind": "task", "name": "PFMBench ANTI-RES: Antibiotic resistance", "status": "source_checked", "url": "/database/task/pfmbench-task-anti-res/", "evaluations": 12, "metric_rows": 12, "charts": 1, "charted_metric_rows": 12, "chart_protocol_ids": [ "pfmbench-task-anti-res" ], "state": "charts_available", "source_ids": [ "expansion-p3-pfmbench" ], "source_urls": [ "https://arxiv.org/html/2506.14796v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "pfmbench-task-binding-db", "kind": "task", "name": "PFMBench BINDING-DB: BindingDB", "status": "source_checked", "url": "/database/task/pfmbench-task-binding-db/", "evaluations": 12, "metric_rows": 12, "charts": 1, "charted_metric_rows": 12, "chart_protocol_ids": [ "pfmbench-task-binding-db" ], "state": "charts_available", "source_ids": [ "expansion-p3-pfmbench" ], "source_urls": [ "https://arxiv.org/html/2506.14796v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "pfmbench-task-cloning-clf", "kind": "task", "name": "PFMBench CLONING-CLF: Cloning CLF", "status": "source_checked", "url": "/database/task/pfmbench-task-cloning-clf/", "evaluations": 12, "metric_rows": 12, "charts": 1, "charted_metric_rows": 12, "chart_protocol_ids": [ "pfmbench-task-cloning-clf" ], "state": "charts_available", "source_ids": [ "expansion-p3-pfmbench" ], "source_urls": [ "https://arxiv.org/html/2506.14796v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "pfmbench-task-deeploc2", "kind": "task", "name": "PFMBench DEEPLOC2: DeepLoc2 Multi", "status": "source_checked", "url": "/database/task/pfmbench-task-deeploc2/", "evaluations": 12, "metric_rows": 12, "charts": 1, "charted_metric_rows": 12, "chart_protocol_ids": [ "pfmbench-task-deeploc2" ], "state": "charts_available", "source_ids": [ "expansion-p3-pfmbench" ], "source_urls": [ "https://arxiv.org/html/2506.14796v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "pfmbench-task-deepsol", "kind": "task", "name": "PFMBench DEEPSOL: DeepSol", "status": "source_checked", "url": "/database/task/pfmbench-task-deepsol/", "evaluations": 12, "metric_rows": 12, "charts": 1, "charted_metric_rows": 12, "chart_protocol_ids": [ "pfmbench-task-deepsol" ], "state": "charts_available", "source_ids": [ "expansion-p3-pfmbench" ], "source_urls": [ "https://arxiv.org/html/2506.14796v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "pfmbench-task-ec", "kind": "task", "name": "PFMBench EC: Enzyme Commission", "status": "source_checked", "url": "/database/task/pfmbench-task-ec/", "evaluations": 12, "metric_rows": 12, "charts": 1, "charted_metric_rows": 12, "chart_protocol_ids": [ "pfmbench-task-ec" ], "state": "charts_available", "source_ids": [ "expansion-p3-pfmbench" ], "source_urls": [ "https://arxiv.org/html/2506.14796v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "pfmbench-task-mat-prod", "kind": "task", "name": "PFMBench MAT-PROD: Material production", "status": "source_checked", "url": "/database/task/pfmbench-task-mat-prod/", "evaluations": 12, "metric_rows": 12, "charts": 1, "charted_metric_rows": 12, "chart_protocol_ids": [ "pfmbench-task-mat-prod" ], "state": "charts_available", "source_ids": [ "expansion-p3-pfmbench" ], "source_urls": [ "https://arxiv.org/html/2506.14796v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "pfmbench-task-metal-ion", "kind": "task", "name": "PFMBench METAL-ION: Metal ion binding", "status": "source_checked", "url": "/database/task/pfmbench-task-metal-ion/", "evaluations": 12, "metric_rows": 12, "charts": 1, "charted_metric_rows": 12, "chart_protocol_ids": [ "pfmbench-task-metal-ion" ], "state": "charts_available", "source_ids": [ "expansion-p3-pfmbench" ], "source_urls": [ "https://arxiv.org/html/2506.14796v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "pfmbench-task-pdb-bind", "kind": "task", "name": "PFMBench PDB-BIND: PDBbind", "status": "source_checked", "url": "/database/task/pfmbench-task-pdb-bind/", "evaluations": 12, "metric_rows": 12, "charts": 1, "charted_metric_rows": 12, "chart_protocol_ids": [ "pfmbench-task-pdb-bind" ], "state": "charts_available", "source_ids": [ "expansion-p3-pfmbench" ], "source_urls": [ "https://arxiv.org/html/2506.14796v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "pfmbench-task-proteingym-zs", "kind": "task", "name": "PFMBench PROTEINGYM-ZS: ProteinGym zero-shot variant effect prediction", "status": "source_checked", "url": "/database/task/pfmbench-task-proteingym-zs/", "evaluations": 9, "metric_rows": 9, "charts": 1, "charted_metric_rows": 9, "chart_protocol_ids": [ "pfmbench-task-proteingym-zs" ], "state": "charts_available", "source_ids": [ "expansion-p3-pfmbench" ], "source_urls": [ "https://arxiv.org/html/2506.14796v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "pfmbench-task-sec-struct", "kind": "task", "name": "PFMBench SEC-STRUCT: Secondary structure", "status": "source_checked", "url": "/database/task/pfmbench-task-sec-struct/", "evaluations": 12, "metric_rows": 12, "charts": 1, "charted_metric_rows": 12, "chart_protocol_ids": [ "pfmbench-task-sec-struct" ], "state": "charts_available", "source_ids": [ "expansion-p3-pfmbench" ], "source_urls": [ "https://arxiv.org/html/2506.14796v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "pfmbench-task-stability", "kind": "task", "name": "PFMBench STABILITY: TAPE_Stability", "status": "source_checked", "url": "/database/task/pfmbench-task-stability/", "evaluations": 12, "metric_rows": 12, "charts": 1, "charted_metric_rows": 12, "chart_protocol_ids": [ "pfmbench-task-stability" ], "state": "charts_available", "source_ids": [ "expansion-p3-pfmbench" ], "source_urls": [ "https://arxiv.org/html/2506.14796v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "catalog-task-phage-pathogen-reads", "kind": "task", "name": "Phage / pathogen reads", "status": "discovered", "url": "/database/task/catalog-task-phage-pathogen-reads/", "evaluations": 0, "metric_rows": 0, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_not_yet_collected", "source_ids": [ "catalog-source-prokbert", "catalog-source-metagene-1", "catalog-source-kraken2", "expansion-p3-prokbert", "evidence-official-2efbfaba5a1c09f4f7fa" ], "source_urls": [ "https://github.com/nbrg-ppcu/prokbert", "https://huggingface.co/metagene-ai/METAGENE-1", "https://github.com/DerrickWood/kraken2", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10810988/fullTextXML", "https://github.com/nbrg-ppcu/prokbert/blob/8670ae92b816cff158a0b85647a8dea122e251eb/README.md" ], "research_status": "broad_task_primary_protocol_linked", "research_review_date": "2026-09-17", "gaps": [ "The broad guide has no single common test population. No sequence-design instructions or pathogen enhancement content is needed for detection benchmarking.", "Full paired numerical figure data remain unextracted; no estimated graph heights." ] }, { "id": "reported-task-d1c46526c39983", "kind": "task", "name": "Physically valid protein–ligand pose selection", "status": "needs_review", "url": "/database/task/reported-task-d1c46526c39983/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "molas-2026", "evidence-expansion-p2-molas-2026-d556d47e0f7b" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC13104262/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13104262/fullTextXML" ], "research_status": "source_found_structured_extraction_pending", "research_review_date": "2026-09-17", "gaps": [ "Complete raw table acquired. Source compares selected algorithm versusSBS percohort; gap is derived difference, not new model score. Five-fold means and paired-significance stars do not imply confidence intervals. Structured extraction pending." ] }, { "id": "reported-task-13dfe6b33e71ed", "kind": "task", "name": "polyadenylation site detection", "status": "needs_review", "url": "/database/task/reported-task-13dfe6b33e71ed/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "polya-glm-2025", "evidence-expansion-p2-polya-glm-2025-e9ebd53d8883" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12799945/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12799945/fullTextXML" ], "research_status": "source_found_structured_extraction_pending", "research_review_date": "2026-09-17", "gaps": [ "Raw complete comparison acquired. Few-shot versus fine-tuning and Gene-Gene versus Intergenic-Gene conditions cannot share a chart group; NT100M and 500M are different configurations. Structured extraction pending." ] }, { "id": "catalog-task-protein-design", "kind": "task", "name": "Protein design / inverse folding", "status": "discovered", "url": "/database/task/catalog-task-protein-design/", "evaluations": 0, "metric_rows": 0, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_not_yet_collected", "source_ids": [ "catalog-source-proteinmpnn", "evidence-expansion-p2-proteinmpnn-original-3e9042dc0ac2", "src-discovery-dauparas-proteinmpnn" ], "source_urls": [ "https://github.com/dauparas/ProteinMPNN", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9997061/fullTextXML", "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/README.md" ], "research_status": "broad_task_requires_concrete_protocol_links", "research_review_date": "2026-09-17", "gaps": [ "Protein design is a broad task. ProteinMPNN reports native sequence recovery on 402 backbones and separate noisy-backbone/experimental design evaluations; no general protein-design ranking. New primary paper pinned, concrete protocol extraction required." ] }, { "id": "reported-task-c4a578065f44b2", "kind": "task", "name": "protein function annotation", "status": "needs_review", "url": "/database/task/reported-task-c4a578065f44b2/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "spin-protein-function-2026", "evidence-expansion-spin-protein-function-2026-9701843e" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12970593/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12970593/" ], "research_status": "primary_comparison_tables_located", "research_review_date": "2026-09-17", "gaps": [ "complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.", "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "reported-task-7621fa1be55362", "kind": "task", "name": "protein localization classification", "status": "needs_review", "url": "/database/task/reported-task-7621fa1be55362/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "cell-dino-2025", "expansion-p3-cell-dino-2025", "evidence-task-final-a-cell-dino-2025-pcbi-1013828-s001-pdf" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12826486/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12826486/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12826486/supplementaryFiles" ], "research_status": "primary_comparison_table_screened", "research_review_date": "2026-09-17", "gaps": [ "Table 2 architectures and pretraining datasets differ; HPA-FoV and HPA-SC are separate protocols.", "Do not attach Cell Painting MoA AUPRC to protein localization.", "Table 6 ensembling is five MLPs with threshold/prediction averaging; not the base frozen model alone." ] }, { "id": "reported-task-c7a8a372f77886", "kind": "task", "name": "protein variant fitness prediction", "status": "needs_review", "url": "/database/task/reported-task-c7a8a372f77886/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "esm2-ofs-fitness-2025", "evidence-expansion-p2-esm2-ofs-fitness-2025-085ef646f11b" ], "source_urls": [ "https://journals.aps.org/prxlife/pdf/10.1103/zhx7-hcmm", "https://harvest.aps.org/v2/journals/articles/10.1103/zhx7-hcmm/fulltext" ], "research_status": "source_found_structured_extraction_pending", "research_review_date": "2026-09-17", "gaps": [ "Pinned source PDF retained; source-specific assay aggregation and substitution/indel scope require full table mapping. Existing result preserved; structured extraction pending." ] }, { "id": "reported-task-83be0998084c91", "kind": "task", "name": "protein variant-effect classification", "status": "needs_review", "url": "/database/task/reported-task-83be0998084c91/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "structure-informed-plm-2025", "evidence-expansion-p2-structure-informed-plm-2025-24c7649edc66", "evidence-benchmark-structure-informed-html" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12068927/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12068927/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12068927/" ], "research_status": "source_found_structured_extraction_pending", "research_review_date": "2026-09-17", "gaps": [ "Artifact returned HTML rather than XML, so XML table parser intentionally rejected it. Prior reviewed observation retained. Complete table extraction and source-version comparison remain pending." ] }, { "id": "reported-task-77a32496ce8fe6", "kind": "task", "name": "protein-ligand binding affinity prediction", "status": "needs_review", "url": "/database/task/reported-task-77a32496ce8fe6/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "ligand-affinity-meta-model-2024", "evidence-expansion-ligand-affinity-meta-model-2024-0be25fe7" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC11632770/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC11632770/" ], "research_status": "primary_comparison_tables_located", "research_review_date": "2026-09-17", "gaps": [ "complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.", "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "reported-task-f0ed5188dbb6d4", "kind": "task", "name": "protein-protein binding-site prediction", "status": "needs_review", "url": "/database/task/reported-task-f0ed5188dbb6d4/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "protein-binding-sites-2023", "evidence-expansion-protein-binding-sites-2023-491711aa" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC9849350/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC9849350/" ], "research_status": "primary_comparison_tables_located", "research_review_date": "2026-09-17", "gaps": [ "complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.", "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "reported-task-09c3100b77dcc5", "kind": "task", "name": "protein-protein interaction prediction", "status": "needs_review", "url": "/database/task/reported-task-09c3100b77dcc5/", "evaluations": 7, "metric_rows": 34, "charts": 11, "charted_metric_rows": 33, "chart_protocol_ids": [ "paper-protocol-be1c9eab950fb814ec", "paper-protocol-1edc32c80b0223fef1" ], "state": "charts_available", "source_ids": [ "esm2-amp-2025", "part2-esm2-amp-2025" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12392411/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12392411/fullTextXML" ], "research_status": "complete_comparison_tables_extracted_pending_publication_review", "research_review_date": "2026-09-17", "gaps": [ "Independent batch review before import; preserve existing observation identities." ] }, { "id": "reported-task-dfa8f2285dbfa5", "kind": "task", "name": "protein-protein interaction prediction", "status": "needs_review", "url": "/database/task/reported-task-dfa8f2285dbfa5/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "gsmformer-ppi-2026", "evidence-expansion-p2-gsmformer-ppi-2026-9b364b5d73d1" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12873117/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12873117/fullTextXML" ], "research_status": "source_found_structured_extraction_pending", "research_review_date": "2026-09-17", "gaps": [ "Complete raw tables acquired. Tables 3/4 matched four-method experiments;Table 5 combines different datasets and cannot form a common ranking. Units mix percentaccuracy and fractionalmetrics. Structured extraction pending." ] }, { "id": "reported-task-b181ed450cdd41", "kind": "task", "name": "protein-small molecule binding-site prediction", "status": "needs_review", "url": "/database/task/reported-task-b181ed450cdd41/", "evaluations": 12, "metric_rows": 45, "charts": 12, "charted_metric_rows": 44, "chart_protocol_ids": [ "paper-protocol-efe21a629d215d8f9a", "paper-protocol-07cf559d2f1f9262e7", "paper-protocol-89b76bfabd1dfe31a6" ], "state": "charts_available", "source_ids": [ "clape-smb-2024", "evidence-expansion-clape-smb-2024-21591924" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC11542454/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC11542454/" ], "research_status": "complete_tables_extracted", "research_review_date": "2026-09-17", "gaps": [ "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "reported-task-d81be76396e644", "kind": "task", "name": "Protein–ligand binding affinity prediction", "status": "needs_review", "url": "/database/task/reported-task-d81be76396e644/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "deelig-2021", "evidence-expansion-p2-deelig-2021-5a7620c18d06" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC8274096/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC8274096/fullTextXML" ], "research_status": "source_found_structured_extraction_pending", "research_review_date": "2026-09-17", "gaps": [ "Complete raw tables acquired. Table 1PCC footnote sayspercentcorrectclassification whileTable 2 labelsPearson; ambiguity quarantined. Literature comparison rows have different training histories. Structured extraction pending." ] }, { "id": "reported-task-a78312d5df6dad", "kind": "task", "name": "Protein–ligand binding affinity scoring", "status": "needs_review", "url": "/database/task/reported-task-a78312d5df6dad/", "evaluations": 37, "metric_rows": 82, "charts": 9, "charted_metric_rows": 81, "chart_protocol_ids": [ "paper-protocol-d2055666ed2da8d7d7", "paper-protocol-31d4bca49fb09d2e6f", "paper-protocol-0c5a1c5ef6896a2d96", "paper-protocol-9e3344661a0f282e5e" ], "state": "charts_available", "source_ids": [ "akscore-2020", "evidence-expansion-akscore-2020-40cfd28d" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC7697539/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC7697539/" ], "research_status": "complete_tables_extracted", "research_review_date": "2026-09-17", "gaps": [ "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "reported-task-94802534b7026d", "kind": "task", "name": "Protein–ligand binding energy prediction", "status": "needs_review", "url": "/database/task/reported-task-94802534b7026d/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "fingerprint-scoring-2022", "expansion-p3-fingerprint-scoring-2022" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC9178954/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC9178954/" ], "research_status": "primary_comparison_table_screened", "research_review_date": "2026-09-17", "gaps": [ "RMSE is lower-is-better; do not mix correlation and energy errors.", "Conventional-function rows must retain software suffixes and scoring settings; exact common test/context needs methods review before merging Tables 1–2 into one chart." ] }, { "id": "catalog-task-ligand-pose", "kind": "task", "name": "Protein–ligand pose", "status": "discovered", "url": "/database/task/catalog-task-ligand-pose/", "evaluations": 0, "metric_rows": 0, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_not_yet_collected", "source_ids": [ "catalog-source-chai-1", "catalog-source-boltz-2", "catalog-source-diffdock-l", "catalog-source-alphafold-3-server", "catalog-source-vina", "evidence-expansion-alphafold3-e627083f", "evidence-expansion-boltz-stereochemistry-2025-78a77b9a", "src-discovery-maabuu-posebusters", "src-discovery-plinder-org-plinder" ], "source_urls": [ "https://github.com/chaidiscovery/chai-lab", "https://github.com/jwohlwend/boltz", "https://github.com/gcorso/DiffDock", "https://alphafoldserver.com/output-terms", "https://github.com/ccsb-scripps/AutoDock-Vina", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11168924/fullTextXML", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12658688/", "https://github.com/maabuu/posebusters/blob/6236d07017493531851cce775e8ef834d4763d2f/README.md", "https://github.com/plinder-org/plinder/blob/85b3f1cb1763530a6cfd934f4263a1777c41afa4/README.md" ], "research_status": "primary_protocol_reviewed", "research_review_date": "2026-09-17", "gaps": [ "complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows." ] }, { "id": "reported-task-bf513ed6db92c5", "kind": "task", "name": "Protein–ligand pose prediction", "status": "needs_review", "url": "/database/task/reported-task-bf513ed6db92c5/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "boltz-stereochemistry-2025", "evidence-expansion-boltz-stereochemistry-2025-78a77b9a" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12658688/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12658688/" ], "research_status": "primary_comparison_tables_located", "research_review_date": "2026-09-17", "gaps": [ "complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.", "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "reported-task-c04bb5ee6ecea6", "kind": "task", "name": "Protein–ligand pose prediction", "status": "needs_review", "url": "/database/task/reported-task-c04bb5ee6ecea6/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "boltz1-2025", "evidence-expansion-p2-boltz1-2025-1ebf712314d9" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC11601547/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11601547/fullTextXML" ], "research_status": "source_found_structured_extraction_pending", "research_review_date": "2026-09-17", "gaps": [ "Pose benchmark values are mainly in figures; Table 1 reports ablation/cycling conditions and cannot substitute for complete competitor pose matrix. Source artifacts acquired; no scores estimated from pixels." ] }, { "id": "reported-task-a7803ecf7708cc", "kind": "task", "name": "Protein–ligand virtual screening", "status": "needs_review", "url": "/database/task/reported-task-a7803ecf7708cc/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "nmdn-2025", "expansion-p3-nmdn-2025" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC11815853/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC11815853/" ], "research_status": "primary_comparison_table_screened", "research_review_date": "2026-09-17", "gaps": [ "Target-level EF, mean EF and counts above EF cutoffs are separate metrics.", "Do not describe pKd-score or pKd-screen as experimentally calibrated affinity from the EF metric.", "All table scores are conditional on the stated docked poses." ] }, { "id": "proteinbench-task-ab-accuracy-aar", "kind": "task", "name": "ProteinBench AB-ACCURACY-AAR: Accuracy AAR", "status": "source_checked", "url": "/database/task/proteinbench-task-ab-accuracy-aar/", "evaluations": 8, "metric_rows": 8, "charts": 1, "charted_metric_rows": 8, "chart_protocol_ids": [ "proteinbench-task-ab-accuracy-aar" ], "state": "charts_available", "source_ids": [ "expansion-p3-proteinbench" ], "source_urls": [ "https://arxiv.org/html/2409.06744v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "proteinbench-task-ab-accuracy-rmsd", "kind": "task", "name": "ProteinBench AB-ACCURACY-RMSD: Accuracy RMSD", "status": "source_checked", "url": "/database/task/proteinbench-task-ab-accuracy-rmsd/", "evaluations": 8, "metric_rows": 8, "charts": 1, "charted_metric_rows": 8, "chart_protocol_ids": [ "proteinbench-task-ab-accuracy-rmsd" ], "state": "charts_available", "source_ids": [ "expansion-p3-proteinbench" ], "source_urls": [ "https://arxiv.org/html/2409.06744v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "proteinbench-task-ab-accuracy-tm-score", "kind": "task", "name": "ProteinBench AB-ACCURACY-TM-SCORE: Accuracy TM-score", "status": "source_checked", "url": "/database/task/proteinbench-task-ab-accuracy-tm-score/", "evaluations": 8, "metric_rows": 8, "charts": 1, "charted_metric_rows": 8, "chart_protocol_ids": [ "proteinbench-task-ab-accuracy-tm-score" ], "state": "charts_available", "source_ids": [ "expansion-p3-proteinbench" ], "source_urls": [ "https://arxiv.org/html/2409.06744v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "proteinbench-task-ab-functionality-binding-energy", "kind": "task", "name": "ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: Functionality Binding Energy", "status": "source_checked", "url": "/database/task/proteinbench-task-ab-functionality-binding-energy/", "evaluations": 8, "metric_rows": 8, "charts": 1, "charted_metric_rows": 8, "chart_protocol_ids": [ "proteinbench-task-ab-functionality-binding-energy" ], "state": "charts_available", "source_ids": [ "expansion-p3-proteinbench" ], "source_urls": [ "https://arxiv.org/html/2409.06744v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "proteinbench-task-ab-rationality-clashes-inner", "kind": "task", "name": "ProteinBench AB-RATIONALITY-CLASHES-INNER: Rationality Clashes-inner", "status": "source_checked", "url": "/database/task/proteinbench-task-ab-rationality-clashes-inner/", "evaluations": 8, "metric_rows": 8, "charts": 1, "charted_metric_rows": 8, "chart_protocol_ids": [ "proteinbench-task-ab-rationality-clashes-inner" ], "state": "charts_available", "source_ids": [ "expansion-p3-proteinbench" ], "source_urls": [ "https://arxiv.org/html/2409.06744v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. 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Individual observations remain in the results table." ] }, { "id": "proteinbench-task-ab-rationality-cn-score", "kind": "task", "name": "ProteinBench AB-RATIONALITY-CN-SCORE: Rationality CN-score", "status": "source_checked", "url": "/database/task/proteinbench-task-ab-rationality-cn-score/", "evaluations": 8, "metric_rows": 8, "charts": 1, "charted_metric_rows": 8, "chart_protocol_ids": [ "proteinbench-task-ab-rationality-cn-score" ], "state": "charts_available", "source_ids": [ "expansion-p3-proteinbench" ], "source_urls": [ "https://arxiv.org/html/2409.06744v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. 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Individual observations remain in the results table." ] }, { "id": "proteinbench-task-ab-specificity-phr", "kind": "task", "name": "ProteinBench AB-SPECIFICITY-PHR: Specificity PHR", "status": "source_checked", "url": "/database/task/proteinbench-task-ab-specificity-phr/", "evaluations": 8, "metric_rows": 8, "charts": 1, "charted_metric_rows": 8, "chart_protocol_ids": [ "proteinbench-task-ab-specificity-phr" ], "state": "charts_available", "source_ids": [ "expansion-p3-proteinbench" ], "source_urls": [ "https://arxiv.org/html/2409.06744v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. 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Individual observations remain in the results table." ] }, { "id": "proteinbench-task-ab-specificity-seqsim-outer", "kind": "task", "name": "ProteinBench AB-SPECIFICITY-SEQSIM-OUTER: Specificity SeqSim-outer", "status": "source_checked", "url": "/database/task/proteinbench-task-ab-specificity-seqsim-outer/", "evaluations": 8, "metric_rows": 8, "charts": 1, "charted_metric_rows": 8, "chart_protocol_ids": [ "proteinbench-task-ab-specificity-seqsim-outer" ], "state": "charts_available", "source_ids": [ "expansion-p3-proteinbench" ], "source_urls": [ "https://arxiv.org/html/2409.06744v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "proteinbench-task-bb-length-100-diversity-max-clust", "kind": "task", "name": "ProteinBench BB-LENGTH-100-DIVERSITY-MAX-CLUST: length 100, Diversity Max Clust.", "status": "source_checked", "url": "/database/task/proteinbench-task-bb-length-100-diversity-max-clust/", "evaluations": 9, "metric_rows": 9, "charts": 1, "charted_metric_rows": 9, "chart_protocol_ids": [ "proteinbench-task-bb-length-100-diversity-max-clust" ], "state": "charts_available", "source_ids": [ "expansion-p3-proteinbench" ], "source_urls": [ "https://arxiv.org/html/2409.06744v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "proteinbench-task-bb-length-100-diversity-pairwise-tm", "kind": "task", "name": "ProteinBench BB-LENGTH-100-DIVERSITY-PAIRWISE-TM: length 100, Diversity pairwise TM", "status": "source_checked", "url": "/database/task/proteinbench-task-bb-length-100-diversity-pairwise-tm/", "evaluations": 9, "metric_rows": 9, "charts": 1, "charted_metric_rows": 9, "chart_protocol_ids": [ "proteinbench-task-bb-length-100-diversity-pairwise-tm" ], "state": "charts_available", "source_ids": [ "expansion-p3-proteinbench" ], "source_urls": [ "https://arxiv.org/html/2409.06744v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "proteinbench-task-bb-length-100-novelty-max-tm", "kind": "task", "name": "ProteinBench BB-LENGTH-100-NOVELTY-MAX-TM: length 100, Novelty Max TM", "status": "source_checked", "url": "/database/task/proteinbench-task-bb-length-100-novelty-max-tm/", "evaluations": 8, "metric_rows": 8, "charts": 1, "charted_metric_rows": 8, "chart_protocol_ids": [ "proteinbench-task-bb-length-100-novelty-max-tm" ], "state": "charts_available", "source_ids": [ "expansion-p3-proteinbench" ], "source_urls": [ "https://arxiv.org/html/2409.06744v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "proteinbench-task-bb-length-100-quality-scrmsd", "kind": "task", "name": "ProteinBench BB-LENGTH-100-QUALITY-SCRMSD: length 100, Quality scRMSD", "status": "source_checked", "url": "/database/task/proteinbench-task-bb-length-100-quality-scrmsd/", "evaluations": 9, "metric_rows": 9, "charts": 1, "charted_metric_rows": 9, "chart_protocol_ids": [ "proteinbench-task-bb-length-100-quality-scrmsd" ], "state": "charts_available", "source_ids": [ "expansion-p3-proteinbench" ], "source_urls": [ "https://arxiv.org/html/2409.06744v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "proteinbench-task-bb-length-100-quality-sctm", "kind": "task", "name": "ProteinBench BB-LENGTH-100-QUALITY-SCTM: length 100, Quality scTM", "status": "source_checked", "url": "/database/task/proteinbench-task-bb-length-100-quality-sctm/", "evaluations": 9, "metric_rows": 9, "charts": 1, "charted_metric_rows": 9, "chart_protocol_ids": [ "proteinbench-task-bb-length-100-quality-sctm" ], "state": "charts_available", "source_ids": [ "expansion-p3-proteinbench" ], "source_urls": [ "https://arxiv.org/html/2409.06744v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "proteinbench-task-bb-length-300-diversity-max-clust", "kind": "task", "name": "ProteinBench BB-LENGTH-300-DIVERSITY-MAX-CLUST: length 300, Diversity Max Clust.", "status": "source_checked", "url": "/database/task/proteinbench-task-bb-length-300-diversity-max-clust/", "evaluations": 9, "metric_rows": 9, "charts": 1, "charted_metric_rows": 9, "chart_protocol_ids": [ "proteinbench-task-bb-length-300-diversity-max-clust" ], "state": "charts_available", "source_ids": [ "expansion-p3-proteinbench" ], "source_urls": [ "https://arxiv.org/html/2409.06744v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. 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Individual observations remain in the results table." ] }, { "id": "proteinbench-task-bb-length-300-novelty-max-tm", "kind": "task", "name": "ProteinBench BB-LENGTH-300-NOVELTY-MAX-TM: length 300, Novelty Max TM", "status": "source_checked", "url": "/database/task/proteinbench-task-bb-length-300-novelty-max-tm/", "evaluations": 8, "metric_rows": 8, "charts": 1, "charted_metric_rows": 8, "chart_protocol_ids": [ "proteinbench-task-bb-length-300-novelty-max-tm" ], "state": "charts_available", "source_ids": [ "expansion-p3-proteinbench" ], "source_urls": [ "https://arxiv.org/html/2409.06744v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "proteinbench-task-bb-length-300-quality-scrmsd", "kind": "task", "name": "ProteinBench BB-LENGTH-300-QUALITY-SCRMSD: length 300, Quality scRMSD", "status": "source_checked", "url": "/database/task/proteinbench-task-bb-length-300-quality-scrmsd/", "evaluations": 9, "metric_rows": 9, "charts": 1, "charted_metric_rows": 9, "chart_protocol_ids": [ "proteinbench-task-bb-length-300-quality-scrmsd" ], "state": "charts_available", "source_ids": [ "expansion-p3-proteinbench" ], "source_urls": [ "https://arxiv.org/html/2409.06744v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. 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Individual observations remain in the results table." ] }, { "id": "proteingym-task-zs-sub-auc", "kind": "task", "name": "ProteinGym ZS-SUB-AUC: Zero-shot substitutions, AUC", "status": "source_checked", "url": "/database/task/proteingym-task-zs-sub-auc/", "evaluations": 21, "metric_rows": 21, "charts": 1, "charted_metric_rows": 21, "chart_protocol_ids": [ "proteingym-task-zs-sub-auc" ], "state": "charts_available", "source_ids": [ "evidence-expansion-proteingym-a3b08cc4" ], "source_urls": [ "https://papers.nips.cc/paper/2023/file/cac723e5ff29f65e3fcbb0739ae91bee-Paper-Datasets_and_Benchmarks.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "proteingym-task-zs-sub-mcc", "kind": "task", "name": "ProteinGym ZS-SUB-MCC: Zero-shot substitutions, MCC", "status": "source_checked", "url": "/database/task/proteingym-task-zs-sub-mcc/", "evaluations": 21, "metric_rows": 21, "charts": 1, "charted_metric_rows": 21, "chart_protocol_ids": [ "proteingym-task-zs-sub-mcc" ], "state": "charts_available", "source_ids": [ "evidence-expansion-proteingym-a3b08cc4" ], "source_urls": [ "https://papers.nips.cc/paper/2023/file/cac723e5ff29f65e3fcbb0739ae91bee-Paper-Datasets_and_Benchmarks.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "proteingym-task-zs-sub-ndcg", "kind": "task", "name": "ProteinGym ZS-SUB-NDCG: Zero-shot substitutions, NDCG@10%", "status": "source_checked", "url": "/database/task/proteingym-task-zs-sub-ndcg/", "evaluations": 21, "metric_rows": 21, "charts": 1, "charted_metric_rows": 21, "chart_protocol_ids": [ "proteingym-task-zs-sub-ndcg" ], "state": "charts_available", "source_ids": [ "evidence-expansion-proteingym-a3b08cc4" ], "source_urls": [ "https://papers.nips.cc/paper/2023/file/cac723e5ff29f65e3fcbb0739ae91bee-Paper-Datasets_and_Benchmarks.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "proteingym-task-zs-sub-recall", "kind": "task", "name": "ProteinGym ZS-SUB-RECALL: Zero-shot substitutions, top 10% recall", "status": "source_checked", "url": "/database/task/proteingym-task-zs-sub-recall/", "evaluations": 21, "metric_rows": 21, "charts": 1, "charted_metric_rows": 21, "chart_protocol_ids": [ "proteingym-task-zs-sub-recall" ], "state": "charts_available", "source_ids": [ "evidence-expansion-proteingym-a3b08cc4" ], "source_urls": [ "https://papers.nips.cc/paper/2023/file/cac723e5ff29f65e3fcbb0739ae91bee-Paper-Datasets_and_Benchmarks.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "proteingym-task-zs-sub-spearman", "kind": "task", "name": "ProteinGym ZS-SUB-SPEARMAN: Zero-shot substitutions, Spearman", "status": "source_checked", "url": "/database/task/proteingym-task-zs-sub-spearman/", "evaluations": 21, "metric_rows": 21, "charts": 1, "charted_metric_rows": 21, "chart_protocol_ids": [ "proteingym-task-zs-sub-spearman" ], "state": "charts_available", "source_ids": [ "evidence-expansion-proteingym-a3b08cc4" ], "source_urls": [ "https://papers.nips.cc/paper/2023/file/cac723e5ff29f65e3fcbb0739ae91bee-Paper-Datasets_and_Benchmarks.pdf" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "reported-task-cdbee1c9285568", "kind": "task", "name": "regulatory element identification", "status": "needs_review", "url": "/database/task/reported-task-cdbee1c9285568/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "dart-eval-regulatory-2024", "evidence-expansion-dart-eval-regulatory-2024-e5aee5b1" ], "source_urls": [ "https://proceedings.neurips.cc/paper_files/paper/2024/file/71998bfc3217ffe1cca1ee084dfadadd-Paper-Datasets_and_Benchmarks_Track.pdf", "https://proceedings.neurips.cc/paper_files/paper/2024/file/71998bfc3217ffe1cca1ee084dfadadd-Paper-Datasets_and_Benchmarks_Track.pdf" ], "research_status": "primary_comparison_tables_located", "research_review_date": "2026-09-17", "gaps": [ "complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.", "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "reported-task-cd127e56fb1f04", "kind": "task", "name": "regulatory sequence classification", "status": "needs_review", "url": "/database/task/reported-task-cd127e56fb1f04/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "genomic-tokenizer-selection-2025", "expansion-p3-genomic-tokenizer-selection-2025" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12453675/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12453675/" ], "research_status": "primary_comparison_table_screened", "research_review_date": "2026-09-17", "gaps": [ "Models differ in architecture, size and pretraining as well as tokenizer, so Table 2 alone does not isolate tokenizer causality.", "Table 3 offers paired tokenizer comparisons; do not relabel whole-family comparisons as controlled tokenizer ablations.", "No per-cell uncertainty in Table 2." ] }, { "id": "reported-task-b9199a30a0bcb2", "kind": "task", "name": "regulatory-variant scoring", "status": "needs_review", "url": "/database/task/reported-task-b9199a30a0bcb2/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "arsenal-regulatory-dna-2026", "expansion-p3-arsenal-regulatory-dna-2026" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12889687/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12889687/" ], "research_status": "primary_comparison_table_screened", "research_review_date": "2026-09-17", "gaps": [ "These are trained hybrid models, not zero-shot ARSENAL scores.", "Keep QTL cohorts and Pearson/Spearman/AUROC separate; verify printed ± definition before plotting error bars." ] }, { "id": "reported-task-3a3bff34cce634", "kind": "task", "name": "RNA compound-binding site prediction", "status": "needs_review", "url": "/database/task/reported-task-3a3bff34cce634/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "cobra-rna-binding-2026", "expansion-p3-cobra-rna-binding-2026" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12790621/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12790621/" ], "research_status": "primary_comparison_table_screened", "research_review_date": "2026-09-17", "gaps": [ "Baselines in Table 4 are taken from Gao et al., Zhu et al. and Chen et al.; this is a literature comparison, not uniformly rerun methods.", "Do not assign the selected CoBRA pipeline score to RiNALMo alone; absent values are unavailable, not zero." ] }, { "id": "catalog-task-rna-secondary-structure", "kind": "task", "name": "RNA secondary structure", "status": "discovered", "url": "/database/task/catalog-task-rna-secondary-structure/", "evaluations": 40, "metric_rows": 160, "charts": 16, "charted_metric_rows": 160, "chart_protocol_ids": [ "paper-protocol-208a8085432aa64eb2", "paper-protocol-e8a1aa302bb8df1efd", "paper-protocol-4c3af10c18f615709d", "paper-protocol-b8acf180ccd3e67923" ], "state": "charts_available", "source_ids": [ "catalog-source-rna-fm", "catalog-source-rhofold", "bpfold-2025", "evidence-expansion-bpfold-2025-976218bd", "src-discovery-terry-r123-rnabenchmark", "src-discovery-ml4bio-rna-fm" ], "source_urls": [ "https://github.com/ml4bio/RNA-FM", "https://github.com/ml4bio/RhoFold", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12216785/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12216785/", "https://github.com/terry-r123/RNABenchmark/blob/da7f9c7ac3f39605af27e1dfcdf879adba963d79/README.md", "https://github.com/ml4bio/RNA-FM/blob/348951516e0963d22bbb33b3c9fc18c89081d38e/README.md" ], "research_status": "complete_tables_extracted", "research_review_date": "2026-09-17", "gaps": [] }, { "id": "reported-task-016f70615f2cfc", "kind": "task", "name": "RNA secondary structure", "status": "needs_review", "url": "/database/task/reported-task-016f70615f2cfc/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "debfold-2024", "evidence-expansion-p2-debfold-2024-e8f960eafb7f" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC11094721/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11094721/fullTextXML" ], "research_status": "source_found_structured_extraction_pending", "research_review_date": "2026-09-17", "gaps": [ "Full raw tables acquired. Different family-held-out cohorts and median-over-three versus median-over-two aggregates must stay distinct. Repeated DEBFold row in Table 2 is not new independent evidence; comRNA missing predictions retained. Structured extraction pending." ] }, { "id": "reported-task-5ec7581b246ea6", "kind": "task", "name": "RNA secondary structure", "status": "needs_review", "url": "/database/task/reported-task-5ec7581b246ea6/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "tu-fold-2025", "evidence-expansion-p2-tu-fold-2025-5aa376d6466d" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12008525/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12008525/fullTextXML" ], "research_status": "source_found_structured_extraction_pending", "research_review_date": "2026-09-17", "gaps": [ "Complete raw comparison acquired,11 methods across overall and two length bands; means/SD preserved. F1/INF and precision/recall separate columns; no aggregate across different length cohorts. Structured extraction pending." ] }, { "id": "reported-task-dc82fcbfb44935", "kind": "task", "name": "RNA secondary structure", "status": "needs_review", "url": "/database/task/reported-task-dc82fcbfb44935/", "evaluations": 40, "metric_rows": 160, "charts": 16, "charted_metric_rows": 160, "chart_protocol_ids": [ "paper-protocol-208a8085432aa64eb2", "paper-protocol-e8a1aa302bb8df1efd", "paper-protocol-4c3af10c18f615709d", "paper-protocol-b8acf180ccd3e67923" ], "state": "charts_available", "source_ids": [ "bpfold-2025", "evidence-expansion-bpfold-2025-976218bd" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12216785/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12216785/" ], "research_status": "complete_tables_extracted", "research_review_date": "2026-09-17", "gaps": [ "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "reported-task-a2bf7ddbc71d23", "kind": "task", "name": "RNA secondary-structure prediction", "status": "needs_review", "url": "/database/task/reported-task-a2bf7ddbc71d23/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "ernie-rna-2025", "evidence-expansion-ernie-rna-2025-0bd1d4b3" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12627772/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12627772/" ], "research_status": "primary_comparison_tables_located", "research_review_date": "2026-09-17", "gaps": [ "complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.", "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "reported-task-df18c710f45213", "kind": "task", "name": "RNA sequence design", "status": "needs_review", "url": "/database/task/reported-task-df18c710f45213/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "r3design-2025", "evidence-expansion-r3design-2025-b49c9ad8" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC11685104/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC11685104/" ], "research_status": "primary_comparison_tables_located", "research_review_date": "2026-09-17", "gaps": [ "complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.", "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "catalog-task-rna-splice-sites", "kind": "task", "name": "RNA splice-site mapping", "status": "discovered", "url": "/database/task/catalog-task-rna-splice-sites/", "evaluations": 0, "metric_rows": 0, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_not_yet_collected", "source_ids": [ "catalog-source-rna-fm", "catalog-source-mimic", "evidence-expansion-gue-49300ace", "evidence-expansion-splice-evaluation-6960a140", "src-discovery-terry-r123-rnabenchmark" ], "source_urls": [ "https://github.com/ml4bio/RNA-FM", "https://huggingface.co/polymathic-ai/MIMIC", "https://arxiv.org/pdf/2306.15006", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10187268/fullTextXML", "https://github.com/terry-r123/RNABenchmark/blob/da7f9c7ac3f39605af27e1dfcdf879adba963d79/README.md" ], "research_status": "primary_protocol_reviewed", "research_review_date": "2026-09-17", "gaps": [ "complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows." ] }, { "id": "catalog-task-rna-tertiary-structure", "kind": "task", "name": "RNA tertiary structure", "status": "discovered", "url": "/database/task/catalog-task-rna-tertiary-structure/", "evaluations": 0, "metric_rows": 0, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_not_yet_collected", "source_ids": [ "catalog-source-rna-fm", "catalog-source-rhofold", "evidence-expansion-alphafold3-e627083f", "src-discovery-ml4bio-rna-fm", "evidence-alphafold-paper" ], "source_urls": [ "https://github.com/ml4bio/RNA-FM", "https://github.com/ml4bio/RhoFold", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11168924/fullTextXML", "https://github.com/ml4bio/RNA-FM/blob/348951516e0963d22bbb33b3c9fc18c89081d38e/README.md", "https://pmc.ncbi.nlm.nih.gov/articles/PMC11168924/" ], "research_status": "primary_protocol_reviewed", "research_review_date": "2026-09-17", "gaps": [ "complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows." ] }, { "id": "reported-task-b00a636d1ed8d9", "kind": "task", "name": "RNA-small-molecule binding-site prediction", "status": "needs_review", "url": "/database/task/reported-task-b00a636d1ed8d9/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "rlsite-rna-binding-2025", "expansion-p3-rlsite-rna-binding-2025" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12417085/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12417085/" ], "research_status": "primary_comparison_table_screened", "research_review_date": "2026-09-17", "gaps": [ "Most baseline values are copied from original publications; RNABind is a web-server run.", "T18/T3/T10 are separate protocols and cannot be pooled as one model score.", "Unavailable RNet AUC is a dash, not zero." ] }, { "id": "reported-task-369dcfef14c4a9", "kind": "task", "name": "Simulated metagenome virus-taxon retrieval", "status": "needs_review", "url": "/database/task/reported-task-369dcfef14c4a9/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "lazypipe-2020", "evidence-expansion-lazypipe-2020-77842d8e" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC7772471/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC7772471/" ], "research_status": "primary_comparison_tables_located", "research_review_date": "2026-09-17", "gaps": [ "complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.", "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "reported-task-53e3d216eef6db", "kind": "task", "name": "Simulated prophage-contig detection", "status": "needs_review", "url": "/database/task/reported-task-53e3d216eef6db/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "viral-contig-simulation-2021", "expansion-p3-viral-contig-simulation-2021" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC8207588/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC8207588/" ], "research_status": "primary_comparison_table_screened", "research_review_date": "2026-09-17", "gaps": [ "Performance averages over simulation conditions, not independent training seeds; do not use rank as a probability.", "Benchmark simulation conditions differ from real metagenomic samples." ] }, { "id": "catalog-task-ligand-affinity", "kind": "task", "name": "Small-molecule affinity", "status": "discovered", "url": "/database/task/catalog-task-ligand-affinity/", "evaluations": 0, "metric_rows": 0, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_not_yet_collected", "source_ids": [ "catalog-source-boltz-2", "expansion-p3-boltz2", "evidence-official-5a9e55abdf288d9dd8da", "src-discovery-plinder-org-plinder" ], "source_urls": [ "https://github.com/jwohlwend/boltz", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12262699/fullTextXML", "https://github.com/jwohlwend/boltz/blob/b1ebfc46ecf57f5414e0d1a6f9027bbb122c53bc/docs/prediction.md", "https://github.com/plinder-org/plinder/blob/85b3f1cb1763530a6cfd934f4263a1777c41afa4/README.md" ], "research_status": "broad_task_primary_protocol_linked", "research_review_date": "2026-09-17", "gaps": [ "Binding probability, mixed-measure affinity regression and virtual-screening enrichment are different outcomes.", "Affinity head mixes biochemical quantities; values are not automatically assay-calibrated Kd.", "No paper-wide universal affinity score or common ligand denominator." ] }, { "id": "reported-task-571f0a2e7faed3", "kind": "task", "name": "Strain-level abundance quantification", "status": "needs_review", "url": "/database/task/reported-task-571f0a2e7faed3/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "cammiq-2022", "evidence-expansion-p2-cammiq-2022-f0939647ed3d", "evidence-task-final-a-cammiq-2022-41467-2022-33869-moesm1-esm-pdf" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC9616933/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9616933/fullTextXML", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9616933/supplementaryFiles" ], "research_status": "source_found_structured_extraction_pending", "research_review_date": "2026-09-17", "gaps": [ "Complete raw table acquired. Identified-strain counts/ratios and L1/L2 abundance errors must remain different metrics; MetaPhlAn detection bounds are not exact counts. Structured extraction pending." ] }, { "id": "discovery-benchmark-tape-contact-prediction", "kind": "task", "name": "TAPE Contact Prediction", "status": "discovered", "url": "/database/task/discovery-benchmark-tape-contact-prediction/", "evaluations": 10, "metric_rows": 10, "charts": 1, "charted_metric_rows": 10, "chart_protocol_ids": [ "discovery-benchmark-tape-contact-prediction" ], "state": "charts_available", "source_ids": [ "src-discovery-songlab-cal-tape", "evidence-discovery-final-tape", "evidence-expansion-evidence-discovery-final-tape-6ee0c3e6" ], "source_urls": [ "https://github.com/songlab-cal/tape/blob/6d345c2b2bbf52cd32cf179325c222afd92aec7e/README.md", "https://arxiv.org/pdf/1906.08230v1", "https://arxiv.org/pdf/1906.08230v1" ], "research_status": "complete_tables_extracted", "research_review_date": "2026-09-17", "gaps": [] }, { "id": "discovery-benchmark-tape-fluorescence", "kind": "task", "name": "TAPE Fluorescence", "status": "discovered", "url": "/database/task/discovery-benchmark-tape-fluorescence/", "evaluations": 10, "metric_rows": 10, "charts": 1, "charted_metric_rows": 10, "chart_protocol_ids": [ "discovery-benchmark-tape-fluorescence" ], "state": "charts_available", "source_ids": [ "src-discovery-songlab-cal-tape", "evidence-discovery-final-tape", "evidence-expansion-evidence-discovery-final-tape-6ee0c3e6" ], "source_urls": [ "https://github.com/songlab-cal/tape/blob/6d345c2b2bbf52cd32cf179325c222afd92aec7e/README.md", "https://arxiv.org/pdf/1906.08230v1", "https://arxiv.org/pdf/1906.08230v1" ], "research_status": "complete_tables_extracted", "research_review_date": "2026-09-17", "gaps": [] }, { "id": "discovery-benchmark-tape-remote-homology-detection", "kind": "task", "name": "TAPE Remote Homology Detection", "status": "discovered", "url": "/database/task/discovery-benchmark-tape-remote-homology-detection/", "evaluations": 10, "metric_rows": 10, "charts": 1, "charted_metric_rows": 10, "chart_protocol_ids": [ "discovery-benchmark-tape-remote-homology-detection" ], "state": "charts_available", "source_ids": [ "src-discovery-songlab-cal-tape", "evidence-discovery-final-tape", "evidence-expansion-evidence-discovery-final-tape-6ee0c3e6" ], "source_urls": [ "https://github.com/songlab-cal/tape/blob/6d345c2b2bbf52cd32cf179325c222afd92aec7e/README.md", "https://arxiv.org/pdf/1906.08230v1", "https://arxiv.org/pdf/1906.08230v1" ], "research_status": "complete_tables_extracted", "research_review_date": "2026-09-17", "gaps": [] }, { "id": "discovery-benchmark-tape-secondary-structure", "kind": "task", "name": "TAPE Secondary Structure", "status": "discovered", "url": "/database/task/discovery-benchmark-tape-secondary-structure/", "evaluations": 10, "metric_rows": 10, "charts": 1, "charted_metric_rows": 10, "chart_protocol_ids": [ "discovery-benchmark-tape-secondary-structure" ], "state": "charts_available", "source_ids": [ "src-discovery-songlab-cal-tape", "evidence-discovery-final-tape", "evidence-expansion-evidence-discovery-final-tape-6ee0c3e6" ], "source_urls": [ "https://github.com/songlab-cal/tape/blob/6d345c2b2bbf52cd32cf179325c222afd92aec7e/README.md", "https://arxiv.org/pdf/1906.08230v1", "https://arxiv.org/pdf/1906.08230v1" ], "research_status": "complete_tables_extracted", "research_review_date": "2026-09-17", "gaps": [] }, { "id": "discovery-benchmark-tape-stability", "kind": "task", "name": "TAPE Stability", "status": "discovered", "url": "/database/task/discovery-benchmark-tape-stability/", "evaluations": 10, "metric_rows": 10, "charts": 1, "charted_metric_rows": 10, "chart_protocol_ids": [ "discovery-benchmark-tape-stability" ], "state": "charts_available", "source_ids": [ "src-discovery-songlab-cal-tape", "evidence-discovery-final-tape", "evidence-expansion-evidence-discovery-final-tape-6ee0c3e6" ], "source_urls": [ "https://github.com/songlab-cal/tape/blob/6d345c2b2bbf52cd32cf179325c222afd92aec7e/README.md", "https://arxiv.org/pdf/1906.08230v1", "https://arxiv.org/pdf/1906.08230v1" ], "research_status": "complete_tables_extracted", "research_review_date": "2026-09-17", "gaps": [] }, { "id": "tdc-task-tdc-ames", "kind": "task", "name": "TDC ADMET benchmark group TDC-AMES: Toxicity: TDC.AMES", "status": "source_checked", "url": "/database/task/tdc-task-tdc-ames/", "evaluations": 3, "metric_rows": 3, "charts": 1, "charted_metric_rows": 3, "chart_protocol_ids": [ "tdc-task-tdc-ames" ], "state": "charts_available", "source_ids": [ "evidence-expansion-tdc-cached-v1-aaa5526f" ], "source_urls": [ "https://arxiv.org/pdf/2102.09548v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "tdc-task-tdc-aqsol", "kind": "task", "name": "TDC ADMET benchmark group TDC-AQSOL: Absorption: TDC.AqSol", "status": "source_checked", "url": "/database/task/tdc-task-tdc-aqsol/", "evaluations": 3, "metric_rows": 3, "charts": 1, "charted_metric_rows": 3, "chart_protocol_ids": [ "tdc-task-tdc-aqsol" ], "state": "charts_available", "source_ids": [ "evidence-expansion-tdc-cached-v1-aaa5526f" ], "source_urls": [ "https://arxiv.org/pdf/2102.09548v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "tdc-task-tdc-bbb", "kind": "task", "name": "TDC ADMET benchmark group TDC-BBB: Distribution: TDC.BBB", "status": "source_checked", "url": "/database/task/tdc-task-tdc-bbb/", "evaluations": 3, "metric_rows": 3, "charts": 1, "charted_metric_rows": 3, "chart_protocol_ids": [ "tdc-task-tdc-bbb" ], "state": "charts_available", "source_ids": [ "evidence-expansion-tdc-cached-v1-aaa5526f" ], "source_urls": [ "https://arxiv.org/pdf/2102.09548v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "tdc-task-tdc-bioav", "kind": "task", "name": "TDC ADMET benchmark group TDC-BIOAV: Absorption: TDC.Bioav", "status": "source_checked", "url": "/database/task/tdc-task-tdc-bioav/", "evaluations": 3, "metric_rows": 3, "charts": 1, "charted_metric_rows": 3, "chart_protocol_ids": [ "tdc-task-tdc-bioav" ], "state": "charts_available", "source_ids": [ "evidence-expansion-tdc-cached-v1-aaa5526f" ], "source_urls": [ "https://arxiv.org/pdf/2102.09548v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "tdc-task-tdc-caco2", "kind": "task", "name": "TDC ADMET benchmark group TDC-CACO2: Absorption: TDC.Caco2", "status": "source_checked", "url": "/database/task/tdc-task-tdc-caco2/", "evaluations": 3, "metric_rows": 3, "charts": 1, "charted_metric_rows": 3, "chart_protocol_ids": [ "tdc-task-tdc-caco2" ], "state": "charts_available", "source_ids": [ "evidence-expansion-tdc-cached-v1-aaa5526f" ], "source_urls": [ "https://arxiv.org/pdf/2102.09548v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "tdc-task-tdc-cl-hepa", "kind": "task", "name": "TDC ADMET benchmark group TDC-CL-HEPA: Excretion: TDC.CL-Hepa", "status": "source_checked", "url": "/database/task/tdc-task-tdc-cl-hepa/", "evaluations": 3, "metric_rows": 3, "charts": 1, "charted_metric_rows": 3, "chart_protocol_ids": [ "tdc-task-tdc-cl-hepa" ], "state": "charts_available", "source_ids": [ "evidence-expansion-tdc-cached-v1-aaa5526f" ], "source_urls": [ "https://arxiv.org/pdf/2102.09548v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "tdc-task-tdc-cl-micro", "kind": "task", "name": "TDC ADMET benchmark group TDC-CL-MICRO: Excretion: TDC.CL-Micro", "status": "source_checked", "url": "/database/task/tdc-task-tdc-cl-micro/", "evaluations": 3, "metric_rows": 3, "charts": 1, "charted_metric_rows": 3, "chart_protocol_ids": [ "tdc-task-tdc-cl-micro" ], "state": "charts_available", "source_ids": [ "evidence-expansion-tdc-cached-v1-aaa5526f" ], "source_urls": [ "https://arxiv.org/pdf/2102.09548v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "tdc-task-tdc-cyp2c9-inhibition", "kind": "task", "name": "TDC ADMET benchmark group TDC-CYP2C9-INHIBITION: Metabolism: TDC.CYP2C9 Inhibition", "status": "source_checked", "url": "/database/task/tdc-task-tdc-cyp2c9-inhibition/", "evaluations": 3, "metric_rows": 3, "charts": 1, "charted_metric_rows": 3, "chart_protocol_ids": [ "tdc-task-tdc-cyp2c9-inhibition" ], "state": "charts_available", "source_ids": [ "evidence-expansion-tdc-cached-v1-aaa5526f" ], "source_urls": [ "https://arxiv.org/pdf/2102.09548v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "tdc-task-tdc-cyp2c9-substrate", "kind": "task", "name": "TDC ADMET benchmark group TDC-CYP2C9-SUBSTRATE: Metabolism: TDC.CYP2C9 Substrate", "status": "source_checked", "url": "/database/task/tdc-task-tdc-cyp2c9-substrate/", "evaluations": 3, "metric_rows": 3, "charts": 1, "charted_metric_rows": 3, "chart_protocol_ids": [ "tdc-task-tdc-cyp2c9-substrate" ], "state": "charts_available", "source_ids": [ "evidence-expansion-tdc-cached-v1-aaa5526f" ], "source_urls": [ "https://arxiv.org/pdf/2102.09548v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "tdc-task-tdc-cyp2d6-inhibition", "kind": "task", "name": "TDC ADMET benchmark group TDC-CYP2D6-INHIBITION: Metabolism: TDC.CYP2D6 Inhibition", "status": "source_checked", "url": "/database/task/tdc-task-tdc-cyp2d6-inhibition/", "evaluations": 3, "metric_rows": 3, "charts": 1, "charted_metric_rows": 3, "chart_protocol_ids": [ "tdc-task-tdc-cyp2d6-inhibition" ], "state": "charts_available", "source_ids": [ "evidence-expansion-tdc-cached-v1-aaa5526f" ], "source_urls": [ "https://arxiv.org/pdf/2102.09548v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "tdc-task-tdc-cyp2d6-substrate", "kind": "task", "name": "TDC ADMET benchmark group TDC-CYP2D6-SUBSTRATE: Metabolism: TDC.CYP2D6 Substrate", "status": "source_checked", "url": "/database/task/tdc-task-tdc-cyp2d6-substrate/", "evaluations": 3, "metric_rows": 3, "charts": 1, "charted_metric_rows": 3, "chart_protocol_ids": [ "tdc-task-tdc-cyp2d6-substrate" ], "state": "charts_available", "source_ids": [ "evidence-expansion-tdc-cached-v1-aaa5526f" ], "source_urls": [ "https://arxiv.org/pdf/2102.09548v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "tdc-task-tdc-cyp3a4-inhibition", "kind": "task", "name": "TDC ADMET benchmark group TDC-CYP3A4-INHIBITION: Metabolism: TDC.CYP3A4 Inhibition", "status": "source_checked", "url": "/database/task/tdc-task-tdc-cyp3a4-inhibition/", "evaluations": 3, "metric_rows": 3, "charts": 1, "charted_metric_rows": 3, "chart_protocol_ids": [ "tdc-task-tdc-cyp3a4-inhibition" ], "state": "charts_available", "source_ids": [ "evidence-expansion-tdc-cached-v1-aaa5526f" ], "source_urls": [ "https://arxiv.org/pdf/2102.09548v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "tdc-task-tdc-cyp3a4-substrate", "kind": "task", "name": "TDC ADMET benchmark group TDC-CYP3A4-SUBSTRATE: Metabolism: TDC.CYP3A4 Substrate", "status": "source_checked", "url": "/database/task/tdc-task-tdc-cyp3a4-substrate/", "evaluations": 3, "metric_rows": 3, "charts": 1, "charted_metric_rows": 3, "chart_protocol_ids": [ "tdc-task-tdc-cyp3a4-substrate" ], "state": "charts_available", "source_ids": [ "evidence-expansion-tdc-cached-v1-aaa5526f" ], "source_urls": [ "https://arxiv.org/pdf/2102.09548v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "tdc-task-tdc-dili", "kind": "task", "name": "TDC ADMET benchmark group TDC-DILI: Toxicity: TDC.DILI", "status": "source_checked", "url": "/database/task/tdc-task-tdc-dili/", "evaluations": 3, "metric_rows": 3, "charts": 1, "charted_metric_rows": 3, "chart_protocol_ids": [ "tdc-task-tdc-dili" ], "state": "charts_available", "source_ids": [ "evidence-expansion-tdc-cached-v1-aaa5526f" ], "source_urls": [ "https://arxiv.org/pdf/2102.09548v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "tdc-task-tdc-half-life", "kind": "task", "name": "TDC ADMET benchmark group TDC-HALF-LIFE: Excretion: TDC.Half Life", "status": "source_checked", "url": "/database/task/tdc-task-tdc-half-life/", "evaluations": 3, "metric_rows": 3, "charts": 1, "charted_metric_rows": 3, "chart_protocol_ids": [ "tdc-task-tdc-half-life" ], "state": "charts_available", "source_ids": [ "evidence-expansion-tdc-cached-v1-aaa5526f" ], "source_urls": [ "https://arxiv.org/pdf/2102.09548v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "tdc-task-tdc-herg", "kind": "task", "name": "TDC ADMET benchmark group TDC-HERG: Toxicity: TDC.hERG", "status": "source_checked", "url": "/database/task/tdc-task-tdc-herg/", "evaluations": 3, "metric_rows": 3, "charts": 1, "charted_metric_rows": 3, "chart_protocol_ids": [ "tdc-task-tdc-herg" ], "state": "charts_available", "source_ids": [ "evidence-expansion-tdc-cached-v1-aaa5526f" ], "source_urls": [ "https://arxiv.org/pdf/2102.09548v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "tdc-task-tdc-hia", "kind": "task", "name": "TDC ADMET benchmark group TDC-HIA: Absorption: TDC.HIA", "status": "source_checked", "url": "/database/task/tdc-task-tdc-hia/", "evaluations": 3, "metric_rows": 3, "charts": 1, "charted_metric_rows": 3, "chart_protocol_ids": [ "tdc-task-tdc-hia" ], "state": "charts_available", "source_ids": [ "evidence-expansion-tdc-cached-v1-aaa5526f" ], "source_urls": [ "https://arxiv.org/pdf/2102.09548v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "tdc-task-tdc-ld50", "kind": "task", "name": "TDC ADMET benchmark group TDC-LD50: Toxicity: TDC.LD50", "status": "source_checked", "url": "/database/task/tdc-task-tdc-ld50/", "evaluations": 3, "metric_rows": 3, "charts": 1, "charted_metric_rows": 3, "chart_protocol_ids": [ "tdc-task-tdc-ld50" ], "state": "charts_available", "source_ids": [ "evidence-expansion-tdc-cached-v1-aaa5526f" ], "source_urls": [ "https://arxiv.org/pdf/2102.09548v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "tdc-task-tdc-lipo", "kind": "task", "name": "TDC ADMET benchmark group TDC-LIPO: Absorption: TDC.Lipo", "status": "source_checked", "url": "/database/task/tdc-task-tdc-lipo/", "evaluations": 3, "metric_rows": 3, "charts": 1, "charted_metric_rows": 3, "chart_protocol_ids": [ "tdc-task-tdc-lipo" ], "state": "charts_available", "source_ids": [ "evidence-expansion-tdc-cached-v1-aaa5526f" ], "source_urls": [ "https://arxiv.org/pdf/2102.09548v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "tdc-task-tdc-pgp", "kind": "task", "name": "TDC ADMET benchmark group TDC-PGP: Absorption: TDC.Pgp", "status": "source_checked", "url": "/database/task/tdc-task-tdc-pgp/", "evaluations": 3, "metric_rows": 3, "charts": 1, "charted_metric_rows": 3, "chart_protocol_ids": [ "tdc-task-tdc-pgp" ], "state": "charts_available", "source_ids": [ "evidence-expansion-tdc-cached-v1-aaa5526f" ], "source_urls": [ "https://arxiv.org/pdf/2102.09548v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "tdc-task-tdc-ppbr", "kind": "task", "name": "TDC ADMET benchmark group TDC-PPBR: Distribution: TDC.PPBR", "status": "source_checked", "url": "/database/task/tdc-task-tdc-ppbr/", "evaluations": 3, "metric_rows": 3, "charts": 1, "charted_metric_rows": 3, "chart_protocol_ids": [ "tdc-task-tdc-ppbr" ], "state": "charts_available", "source_ids": [ "evidence-expansion-tdc-cached-v1-aaa5526f" ], "source_urls": [ "https://arxiv.org/pdf/2102.09548v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "tdc-task-tdc-vd", "kind": "task", "name": "TDC ADMET benchmark group TDC-VD: Distribution: TDC.VDss", "status": "source_checked", "url": "/database/task/tdc-task-tdc-vd/", "evaluations": 3, "metric_rows": 3, "charts": 1, "charted_metric_rows": 3, "chart_protocol_ids": [ "tdc-task-tdc-vd" ], "state": "charts_available", "source_ids": [ "evidence-expansion-tdc-cached-v1-aaa5526f" ], "source_urls": [ "https://arxiv.org/pdf/2102.09548v1" ], "research_status": "No separate paper-extraction audit recorded", "research_review_date": null, "gaps": [ "Only reviewed, source-scoped comparison groups are charted. Individual observations remain in the results table." ] }, { "id": "reported-task-ac191e878dff5e", "kind": "task", "name": "transcription-factor DNA binding-site prediction", "status": "needs_review", "url": "/database/task/reported-task-ac191e878dff5e/", "evaluations": 6, "metric_rows": 12, "charts": 2, "charted_metric_rows": 12, "chart_protocol_ids": [ "paper-protocol-6821afc366eb11d0c6" ], "state": "charts_available", "source_ids": [ "transbind-2026", "part2-transbind-2026" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC13145115/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13145115/fullTextXML" ], "research_status": "complete_comparison_tables_extracted_pending_publication_review", "research_review_date": "2026-09-17", "gaps": [ "Independent batch review before import; preserve existing observation identities." ] }, { "id": "catalog-task-utr-translation", "kind": "task", "name": "Translation / RNA stability", "status": "discovered", "url": "/database/task/catalog-task-utr-translation/", "evaluations": 0, "metric_rows": 0, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_not_yet_collected", "source_ids": [ "catalog-source-mrna-fm", "catalog-source-mimic", "evidence-expansion-p2-mrnabench-2025-79f6264ee883", "src-discovery-morrislab-mrnabench" ], "source_urls": [ "https://github.com/ml4bio/RNA-FM", "https://huggingface.co/polymathic-ai/MIMIC", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12265608/fullTextXML", "https://github.com/morrislab/mRNABench/blob/74f96b8e6ae9f41cc3cccff089d826a62d5604b8/README.md" ], "research_status": "broad_task_requires_concrete_protocol_links", "research_review_date": "2026-09-17", "gaps": [ "Translation and stability encompass separate species, cell contexts, transcript regions and assays. Fresh primary XML pinned; concrete mRNABench protocols should be linked instead of attaching all suite results to broad task." ] }, { "id": "reported-task-f7142c3b3e0f3c", "kind": "task", "name": "translation-efficiency prediction", "status": "needs_review", "url": "/database/task/reported-task-f7142c3b3e0f3c/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "mrnabert-2025", "evidence-expansion-mrnabert-2025-ff08ba89", "evidence-task-final-b-mrnabert-supplement" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12644827/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC12644827/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12644827/supplementaryFiles" ], "research_status": "primary_comparison_tables_located", "research_review_date": "2026-09-17", "gaps": [ "complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.", "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "reported-task-4a54ce01b5a855", "kind": "task", "name": "unseen-species genus classification", "status": "needs_review", "url": "/database/task/reported-task-4a54ce01b5a855/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "barcodebert-2026", "expansion-p3-barcodebert-2026" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC13008329/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC13008329/" ], "research_status": "primary_comparison_table_screened", "research_review_date": "2026-09-17", "gaps": [ "Table does not give uncertainty for each genus accuracy; BLAST is an alignment reference, not a pretrained encoder." ] }, { "id": "reported-task-47465954d606e6", "kind": "task", "name": "vaccine-antigen candidate prediction", "status": "needs_review", "url": "/database/task/reported-task-47465954d606e6/", "evaluations": 4, "metric_rows": 22, "charts": 7, "charted_metric_rows": 21, "chart_protocol_ids": [ "paper-protocol-a7bf3c8f6b432c3093" ], "state": "charts_available", "source_ids": [ "vaxign-esm-2024", "part2-vaxign-esm-2024" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC11398487/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11398487/fullTextXML" ], "research_status": "complete_comparison_tables_extracted_pending_publication_review", "research_review_date": "2026-09-17", "gaps": [ "Independent batch review before import; preserve existing observation identities." ] }, { "id": "reported-task-3d4dec23120fef", "kind": "task", "name": "viral sequence detection", "status": "needs_review", "url": "/database/task/reported-task-3d4dec23120fef/", "evaluations": 1, "metric_rows": 1, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "detire-viral-metagenomes-2023", "evidence-expansion-detire-viral-metagenomes-2023-9ff7d327" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC10313334/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC10313334/" ], "research_status": "primary_comparison_tables_located", "research_review_date": "2026-09-17", "gaps": [ "complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.", "exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size." ] }, { "id": "reported-task-6243658a1bc215", "kind": "task", "name": "Zero-shot substitution mutation effects: stability", "status": "needs_review", "url": "/database/task/reported-task-6243658a1bc215/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "proteingym-2023", "expansion-p3-proteingym-2023" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC10723403/", "https://pmc.ncbi.nlm.nih.gov/articles/PMC10723403/" ], "research_status": "primary_comparison_table_screened", "research_review_date": "2026-09-17", "gaps": [ "Other functional-category columns do not belong to the stability benchmark.", "This pinned 2023 paper table is not the latest ProteinGym leaderboard; do not overwrite later-version results.", "MSA and structure inputs differ across model categories; no universal sequence-only ranking." ] }, { "id": "reported-task-a5141363b0ee45", "kind": "task", "name": "Zero-shot variant effect prediction", "status": "needs_review", "url": "/database/task/reported-task-a5141363b0ee45/", "evaluations": 2, "metric_rows": 2, "charts": 0, "charted_metric_rows": 0, "chart_protocol_ids": [], "state": "results_without_validated_comparison", "source_ids": [ "pst-2025", "evidence-expansion-p2-pst-2025-c21ad593de58", "evidence-task-final-b-pst-supplement" ], "source_urls": [ "https://pmc.ncbi.nlm.nih.gov/articles/PMC12603367/", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12603367/fullTextXML", "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12603367/supplementaryFiles" ], "research_status": "existing_observations_cover_named_comparison", "research_review_date": "2026-09-17", "gaps": [ "Table contains two zero-shot mean absolute Spearman values already in catalogue; no new independent observations warranted. Other Table 2 tasks are different benchmarks. Full raw table and source receipt retained." ] } ] }