{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2013:IKH2DKEH4GGHP44FL545M5C3TJ","short_pith_number":"pith:IKH2DKEH","canonical_record":{"source":{"id":"1309.2319","kind":"arxiv","version":2},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.PE","submitted_at":"2013-09-09T20:44:09Z","cross_cats_sorted":["q-bio.QM"],"title_canon_sha256":"3b276f2c8feaf4c0f397f7e33274f9eb5f086f0c1c4b2cd86f82ea8795c16fe6","abstract_canon_sha256":"690b762aea24eabea2e6013520d689eb597a8938c2b06e9a3fbb652c3e441733"},"schema_version":"1.0"},"canonical_sha256":"428fa1a887e18c77f3855f79d6745b9a46a7fd7a60f95d97cb30e4142e6cb281","source":{"kind":"arxiv","id":"1309.2319","version":2},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1309.2319","created_at":"2026-05-18T02:53:53Z"},{"alias_kind":"arxiv_version","alias_value":"1309.2319v2","created_at":"2026-05-18T02:53:53Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1309.2319","created_at":"2026-05-18T02:53:53Z"},{"alias_kind":"pith_short_12","alias_value":"IKH2DKEH4GGH","created_at":"2026-05-18T12:27:46Z"},{"alias_kind":"pith_short_16","alias_value":"IKH2DKEH4GGHP44F","created_at":"2026-05-18T12:27:46Z"},{"alias_kind":"pith_short_8","alias_value":"IKH2DKEH","created_at":"2026-05-18T12:27:46Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2013:IKH2DKEH4GGHP44FL545M5C3TJ","target":"record","payload":{"canonical_record":{"source":{"id":"1309.2319","kind":"arxiv","version":2},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.PE","submitted_at":"2013-09-09T20:44:09Z","cross_cats_sorted":["q-bio.QM"],"title_canon_sha256":"3b276f2c8feaf4c0f397f7e33274f9eb5f086f0c1c4b2cd86f82ea8795c16fe6","abstract_canon_sha256":"690b762aea24eabea2e6013520d689eb597a8938c2b06e9a3fbb652c3e441733"},"schema_version":"1.0"},"canonical_sha256":"428fa1a887e18c77f3855f79d6745b9a46a7fd7a60f95d97cb30e4142e6cb281","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T02:53:53.630447Z","signature_b64":"hj8LuPvpmQwVqTmR0dp5rMFRnijtvUNUmAe0FWja4Dg6Iv3C5Ei5voY/6zh/u1mU0aj6PIrM21e0FH9C6pD+BA==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"428fa1a887e18c77f3855f79d6745b9a46a7fd7a60f95d97cb30e4142e6cb281","last_reissued_at":"2026-05-18T02:53:53.629635Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T02:53:53.629635Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"1309.2319","source_version":2,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-05-18T02:53:53Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"oAYOeEjKImCzZO2GV19XkGck538sBuLryFIMdq2Pwey0TQHl/iq6gpLg4u97qd5dhV+roI/ojqVSKiCqBN5/AQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-06-22T10:42:03.642990Z"},"content_sha256":"7921bf504308ef71751bc0245568bd83e0db877b5772bf7a482353599faa1819","schema_version":"1.0","event_id":"sha256:7921bf504308ef71751bc0245568bd83e0db877b5772bf7a482353599faa1819"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2013:IKH2DKEH4GGHP44FL545M5C3TJ","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"A MOSAIC of methods: Improving ortholog detection through integration of algorithmic diversity","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["q-bio.QM"],"primary_cat":"q-bio.PE","authors_text":"M. Cyrus Maher, Ryan D. Hernandez","submitted_at":"2013-09-09T20:44:09Z","abstract_excerpt":"Ortholog detection (OD) is a critical step for comparative genomic analysis of protein-coding sequences. In this paper, we begin with a comprehensive comparison of four popular, methodologically diverse OD methods: MultiParanoid, Blat, Multiz, and OMA. In head-to-head comparisons, these methods are shown to significantly outperform one another 12-30% of the time. This high complementarity motivates the presentation of the first tool for integrating methodologically diverse OD methods. We term this program MOSAIC, or Multiple Orthologous Sequence Analysis and Integration by Cluster optimization"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1309.2319","kind":"arxiv","version":2},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"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":"2026-05-18T02:53:53Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"g9oyvBkFxdez6Y1+F4+DLcMSlxkF8dksqPwPHC1E6O6ymnKjBTo01mnE0MuDjjOcfMS/gytrWqJSvBe4kYWGBQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-06-22T10:42:03.643350Z"},"content_sha256":"976fe18c9f1eee70466a04a0f3be50fbc0885e0f1d4afdf6cacd6ce78f6f67b5","schema_version":"1.0","event_id":"sha256:976fe18c9f1eee70466a04a0f3be50fbc0885e0f1d4afdf6cacd6ce78f6f67b5"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/IKH2DKEH4GGHP44FL545M5C3TJ/bundle.json","state_url":"https://pith.science/pith/IKH2DKEH4GGHP44FL545M5C3TJ/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/IKH2DKEH4GGHP44FL545M5C3TJ/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":"2026-06-22T10:42:03Z","links":{"resolver":"https://pith.science/pith/IKH2DKEH4GGHP44FL545M5C3TJ","bundle":"https://pith.science/pith/IKH2DKEH4GGHP44FL545M5C3TJ/bundle.json","state":"https://pith.science/pith/IKH2DKEH4GGHP44FL545M5C3TJ/state.json","well_known_bundle":"https://pith.science/.well-known/pith/IKH2DKEH4GGHP44FL545M5C3TJ/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2013:IKH2DKEH4GGHP44FL545M5C3TJ","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":"690b762aea24eabea2e6013520d689eb597a8938c2b06e9a3fbb652c3e441733","cross_cats_sorted":["q-bio.QM"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.PE","submitted_at":"2013-09-09T20:44:09Z","title_canon_sha256":"3b276f2c8feaf4c0f397f7e33274f9eb5f086f0c1c4b2cd86f82ea8795c16fe6"},"schema_version":"1.0","source":{"id":"1309.2319","kind":"arxiv","version":2}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1309.2319","created_at":"2026-05-18T02:53:53Z"},{"alias_kind":"arxiv_version","alias_value":"1309.2319v2","created_at":"2026-05-18T02:53:53Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1309.2319","created_at":"2026-05-18T02:53:53Z"},{"alias_kind":"pith_short_12","alias_value":"IKH2DKEH4GGH","created_at":"2026-05-18T12:27:46Z"},{"alias_kind":"pith_short_16","alias_value":"IKH2DKEH4GGHP44F","created_at":"2026-05-18T12:27:46Z"},{"alias_kind":"pith_short_8","alias_value":"IKH2DKEH","created_at":"2026-05-18T12:27:46Z"}],"graph_snapshots":[{"event_id":"sha256:976fe18c9f1eee70466a04a0f3be50fbc0885e0f1d4afdf6cacd6ce78f6f67b5","target":"graph","created_at":"2026-05-18T02:53:53Z","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"},"paper":{"abstract_excerpt":"Ortholog detection (OD) is a critical step for comparative genomic analysis of protein-coding sequences. In this paper, we begin with a comprehensive comparison of four popular, methodologically diverse OD methods: MultiParanoid, Blat, Multiz, and OMA. In head-to-head comparisons, these methods are shown to significantly outperform one another 12-30% of the time. This high complementarity motivates the presentation of the first tool for integrating methodologically diverse OD methods. We term this program MOSAIC, or Multiple Orthologous Sequence Analysis and Integration by Cluster optimization","authors_text":"M. Cyrus Maher, Ryan D. Hernandez","cross_cats":["q-bio.QM"],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.PE","submitted_at":"2013-09-09T20:44:09Z","title":"A MOSAIC of methods: Improving ortholog detection through integration of algorithmic diversity"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1309.2319","kind":"arxiv","version":2},"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":"sha256:7921bf504308ef71751bc0245568bd83e0db877b5772bf7a482353599faa1819","target":"record","created_at":"2026-05-18T02:53:53Z","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":"690b762aea24eabea2e6013520d689eb597a8938c2b06e9a3fbb652c3e441733","cross_cats_sorted":["q-bio.QM"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.PE","submitted_at":"2013-09-09T20:44:09Z","title_canon_sha256":"3b276f2c8feaf4c0f397f7e33274f9eb5f086f0c1c4b2cd86f82ea8795c16fe6"},"schema_version":"1.0","source":{"id":"1309.2319","kind":"arxiv","version":2}},"canonical_sha256":"428fa1a887e18c77f3855f79d6745b9a46a7fd7a60f95d97cb30e4142e6cb281","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"428fa1a887e18c77f3855f79d6745b9a46a7fd7a60f95d97cb30e4142e6cb281","first_computed_at":"2026-05-18T02:53:53.629635Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-18T02:53:53.629635Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"hj8LuPvpmQwVqTmR0dp5rMFRnijtvUNUmAe0FWja4Dg6Iv3C5Ei5voY/6zh/u1mU0aj6PIrM21e0FH9C6pD+BA==","signature_status":"signed_v1","signed_at":"2026-05-18T02:53:53.630447Z","signed_message":"canonical_sha256_bytes"},"source_id":"1309.2319","source_kind":"arxiv","source_version":2}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:7921bf504308ef71751bc0245568bd83e0db877b5772bf7a482353599faa1819","sha256:976fe18c9f1eee70466a04a0f3be50fbc0885e0f1d4afdf6cacd6ce78f6f67b5"],"state_sha256":"697f486a4d699951e2d415e3a84ff998d8980ef70093ac267eed95e40e3837e4"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"V+U7A5SDMV314Rk4BfxJjDOB9cNUKYto2JO9QIMIgtnK1JAhOrIywMcOMrqg9LiOME6h8ktoGQV6ri9bg4+YAw==","signed_message":"bundle_sha256_bytes","signed_at":"2026-06-22T10:42:03.645290Z","bundle_sha256":"609460af57f9478260135456e9f54f5b572093f185eaf9c6c7286fe4d8fbbae4"}}