{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2024:2C3QG2R4RG3HHH6D6YAVKIYNPP","short_pith_number":"pith:2C3QG2R4","canonical_record":{"source":{"id":"2412.12688","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","primary_cat":"cs.DB","submitted_at":"2024-12-17T09:08:52Z","cross_cats_sorted":[],"title_canon_sha256":"53f401f907d7aee9bef00835b25dc2f50c77d8975384cf5ebd41b2093d987a62","abstract_canon_sha256":"375850195352e8062aae76ddd3e938fcd02752b40efb3cf8989bf7ee5ed003de"},"schema_version":"1.0"},"canonical_sha256":"d0b7036a3c89b6739fc3f60155230d7bc4252b6963379b749a8d984bac9c9447","source":{"kind":"arxiv","id":"2412.12688","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2412.12688","created_at":"2026-07-05T09:50:19Z"},{"alias_kind":"arxiv_version","alias_value":"2412.12688v1","created_at":"2026-07-05T09:50:19Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2412.12688","created_at":"2026-07-05T09:50:19Z"},{"alias_kind":"pith_short_12","alias_value":"2C3QG2R4RG3H","created_at":"2026-07-05T09:50:19Z"},{"alias_kind":"pith_short_16","alias_value":"2C3QG2R4RG3HHH6D","created_at":"2026-07-05T09:50:19Z"},{"alias_kind":"pith_short_8","alias_value":"2C3QG2R4","created_at":"2026-07-05T09:50:19Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2024:2C3QG2R4RG3HHH6D6YAVKIYNPP","target":"record","payload":{"canonical_record":{"source":{"id":"2412.12688","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","primary_cat":"cs.DB","submitted_at":"2024-12-17T09:08:52Z","cross_cats_sorted":[],"title_canon_sha256":"53f401f907d7aee9bef00835b25dc2f50c77d8975384cf5ebd41b2093d987a62","abstract_canon_sha256":"375850195352e8062aae76ddd3e938fcd02752b40efb3cf8989bf7ee5ed003de"},"schema_version":"1.0"},"canonical_sha256":"d0b7036a3c89b6739fc3f60155230d7bc4252b6963379b749a8d984bac9c9447","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T09:50:19.219218Z","signature_b64":"9mAvxxiGkNircnQCpHiXyuXAGlvtBReB8aOGFdVjd+t7IguuJ/hRyyRkXcCy8wzzScabEV3sI9i6mlomakUTDw==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"d0b7036a3c89b6739fc3f60155230d7bc4252b6963379b749a8d984bac9c9447","last_reissued_at":"2026-07-05T09:50:19.218857Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T09:50:19.218857Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2412.12688","source_version":1,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-07-05T09:50:19Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"iZ2E0QhyOFla2o9B5PHoVz+IYedOcAuVyXuMW9UDuTjLlOgNBnXzTdIdKn0DDK5MMeNhNbSE9Lj1kvm7RSeBAQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-07-16T23:11:44.568564Z"},"content_sha256":"2ee56d2c6cdfb071dd929313fc10eeeaa5604aae91d8be390704cb1ca48a2f20","schema_version":"1.0","event_id":"sha256:2ee56d2c6cdfb071dd929313fc10eeeaa5604aae91d8be390704cb1ca48a2f20"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2024:2C3QG2R4RG3HHH6D6YAVKIYNPP","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers","license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","headline":"","cross_cats":[],"primary_cat":"cs.DB","authors_text":"Feng Jiang, Hehuan Ma, Jean Gao, Jingquan Yan, Junzhou Huang, Weizhi An, Yuwei Miao, Yuzhi Guo","submitted_at":"2024-12-17T09:08:52Z","abstract_excerpt":"Gene studies are crucial for fields such as protein structure prediction, drug discovery, and cancer genomics, yet they face challenges in fully utilizing the vast and diverse information available. Gene studies require clean, factual datasets to ensure reliable results. Ontology graphs, neatly organized domain terminology graphs, provide ideal sources for domain facts. However, available gene ontology annotations are currently distributed across various databases without unified identifiers for genes and gene products. To address these challenges, we introduce Unified Entrez Gene Identifier D"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2412.12688","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2412.12688/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"},"verdict_id":null},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-07-05T09:50:19Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"dxRK6Ut9RBpWINBsti7OXd+9xVbBGv42Jg1zPSMXf2QpSMYCjd3BsBCmjidbJSzVQ3zYAVvftjejJekVrh+ODA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-07-16T23:11:44.568922Z"},"content_sha256":"a3f3049b4776ad2300cc6de562dcf66b0ccb0e584b59374164194b82bfd5bdd2","schema_version":"1.0","event_id":"sha256:a3f3049b4776ad2300cc6de562dcf66b0ccb0e584b59374164194b82bfd5bdd2"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/2C3QG2R4RG3HHH6D6YAVKIYNPP/bundle.json","state_url":"https://pith.science/pith/2C3QG2R4RG3HHH6D6YAVKIYNPP/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/2C3QG2R4RG3HHH6D6YAVKIYNPP/bundle.json","status":"primary"}],"public_keys":[{"key_id":"pith-v1-2026-05","algorithm":"ed25519","format":"raw","public_key_b64":"stVStoiQhXFxp4s2pdzPNoqVNBMojDU/fJ2db5S3CbM=","public_key_hex":"b2d552b68890857171a78b36a5dccf368a953413288c353f7c9d9d6f94b709b3","fingerprint_sha256_b32_first128bits":"RVFV5Z2OI2J3ZUO7ERDEBCYNKS","fingerprint_sha256_hex":"8d4b5ee74e4693bcd1df2446408b0d54","rotates_at":null,"url":"https://pith.science/pith-signing-key.json","notes":"Pith uses this Ed25519 key to sign canonical record SHA-256 digests. Verify with: ed25519_verify(public_key, message=canonical_sha256_bytes, signature=base64decode(signature_b64))."}],"merge_version":"pith-open-graph-merge-v1","built_at":"2026-07-16T23:11:44Z","links":{"resolver":"https://pith.science/pith/2C3QG2R4RG3HHH6D6YAVKIYNPP","bundle":"https://pith.science/pith/2C3QG2R4RG3HHH6D6YAVKIYNPP/bundle.json","state":"https://pith.science/pith/2C3QG2R4RG3HHH6D6YAVKIYNPP/state.json","well_known_bundle":"https://pith.science/.well-known/pith/2C3QG2R4RG3HHH6D6YAVKIYNPP/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2024:2C3QG2R4RG3HHH6D6YAVKIYNPP","merge_version":"pith-open-graph-merge-v1","event_count":2,"valid_event_count":2,"invalid_event_count":0,"equivocation_count":0,"current":{"canonical_record":{"metadata":{"abstract_canon_sha256":"375850195352e8062aae76ddd3e938fcd02752b40efb3cf8989bf7ee5ed003de","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","primary_cat":"cs.DB","submitted_at":"2024-12-17T09:08:52Z","title_canon_sha256":"53f401f907d7aee9bef00835b25dc2f50c77d8975384cf5ebd41b2093d987a62"},"schema_version":"1.0","source":{"id":"2412.12688","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2412.12688","created_at":"2026-07-05T09:50:19Z"},{"alias_kind":"arxiv_version","alias_value":"2412.12688v1","created_at":"2026-07-05T09:50:19Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2412.12688","created_at":"2026-07-05T09:50:19Z"},{"alias_kind":"pith_short_12","alias_value":"2C3QG2R4RG3H","created_at":"2026-07-05T09:50:19Z"},{"alias_kind":"pith_short_16","alias_value":"2C3QG2R4RG3HHH6D","created_at":"2026-07-05T09:50:19Z"},{"alias_kind":"pith_short_8","alias_value":"2C3QG2R4","created_at":"2026-07-05T09:50:19Z"}],"graph_snapshots":[{"event_id":"sha256:a3f3049b4776ad2300cc6de562dcf66b0ccb0e584b59374164194b82bfd5bdd2","target":"graph","created_at":"2026-07-05T09:50:19Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"graph_snapshot":{"author_claims":{"count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","strong_count":0},"builder_version":"pith-number-builder-2026-05-17-v1","claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"integrity":{"available":true,"clean":true,"detectors_run":[],"endpoint":"/pith/2412.12688/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"Gene studies are crucial for fields such as protein structure prediction, drug discovery, and cancer genomics, yet they face challenges in fully utilizing the vast and diverse information available. Gene studies require clean, factual datasets to ensure reliable results. Ontology graphs, neatly organized domain terminology graphs, provide ideal sources for domain facts. However, available gene ontology annotations are currently distributed across various databases without unified identifiers for genes and gene products. To address these challenges, we introduce Unified Entrez Gene Identifier D","authors_text":"Feng Jiang, Hehuan Ma, Jean Gao, Jingquan Yan, Junzhou Huang, Weizhi An, Yuwei Miao, Yuzhi Guo","cross_cats":[],"headline":"","license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","primary_cat":"cs.DB","submitted_at":"2024-12-17T09:08:52Z","title":"UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2412.12688","kind":"arxiv","version":1},"verdict":{"created_at":null,"id":null,"model_set":{},"one_line_summary":"","pipeline_version":null,"pith_extraction_headline":"","strongest_claim":"","weakest_assumption":""}},"verdict_id":null}}],"author_attestations":[],"timestamp_anchors":[],"storage_attestations":[],"citation_signatures":[],"replication_records":[],"corrections":[],"mirror_hints":[],"record_created":{"event_id":"sha256:2ee56d2c6cdfb071dd929313fc10eeeaa5604aae91d8be390704cb1ca48a2f20","target":"record","created_at":"2026-07-05T09:50:19Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"attestation_state":"computed","canonical_record":{"metadata":{"abstract_canon_sha256":"375850195352e8062aae76ddd3e938fcd02752b40efb3cf8989bf7ee5ed003de","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","primary_cat":"cs.DB","submitted_at":"2024-12-17T09:08:52Z","title_canon_sha256":"53f401f907d7aee9bef00835b25dc2f50c77d8975384cf5ebd41b2093d987a62"},"schema_version":"1.0","source":{"id":"2412.12688","kind":"arxiv","version":1}},"canonical_sha256":"d0b7036a3c89b6739fc3f60155230d7bc4252b6963379b749a8d984bac9c9447","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"d0b7036a3c89b6739fc3f60155230d7bc4252b6963379b749a8d984bac9c9447","first_computed_at":"2026-07-05T09:50:19.218857Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T09:50:19.218857Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"9mAvxxiGkNircnQCpHiXyuXAGlvtBReB8aOGFdVjd+t7IguuJ/hRyyRkXcCy8wzzScabEV3sI9i6mlomakUTDw==","signature_status":"signed_v1","signed_at":"2026-07-05T09:50:19.219218Z","signed_message":"canonical_sha256_bytes"},"source_id":"2412.12688","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:2ee56d2c6cdfb071dd929313fc10eeeaa5604aae91d8be390704cb1ca48a2f20","sha256:a3f3049b4776ad2300cc6de562dcf66b0ccb0e584b59374164194b82bfd5bdd2"],"state_sha256":"50a169b7a8f0bf01e9c15784c6725b5ce453f094ff6271e96545bbabd9ff1f2b"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"CLMsyGY45CGBh2AfZ0+ui9KJDCEWntvq8XJ+xW3Y646ZYP0onsYfl7m9DWQNaToHchSyR+OMLCLyFc5Nmy0eDQ==","signed_message":"bundle_sha256_bytes","signed_at":"2026-07-16T23:11:44.571410Z","bundle_sha256":"229655f20061454d2fd181ddfedf0cdcb7bb4dee0d92ff83d6f4c40354485112"}}