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This labor intensive process has heavily relied on highly trained human experts, which makes it challenging to scale and thus a key bottleneck. Dahdul et al. (2018) established a Gold Standard (GS) of Entity-Quality (EQ) annotations across seven phylogenetic studies and used it to evaluate three human curators and the Semantic CharaParser NLP tool with ontology-based semantic similarity metrics; they reported that machine-human consistency was significantly lower than inter-curator (human-human) consistency. Here we revisit that benchmark with five frontier hosted LLMs from Anthropic and OpenAI, each operating as an \"agentic curator\" within a self-contained workspace that supplies the source publication PDF, the same annotation guide used by the original","title":"Frontier LLM-based agents can overcome the ontology curation bottleneck for natural phenotypes","url":"https://arxiv.org/abs/2605.28965","vendor":"arxiv_cs_ai"},"summary":"arXiv:2605.28965v1 Announce Type: new \nAbstract: Linking free-text phenotype descriptions to ontology terms, typically referred to as phenotype annotation, is essential for the cross-study integration of comparative morphological data. This labor intensive process has heavily relied on highly trained human experts, which makes it challenging to scale and thus a key bottleneck. Dahdul et al. (2018) established a Gold Standard (GS) of Entity-Quality (EQ) annotations across seven phylogenetic studies and used it to evaluate three human curators and the Semantic CharaParser NLP tool with ontology-based semantic similarity metrics; they reported that machine-human consistency was significantly lower than inter-curator (human-human) consistency. Here we revisit that benchmark with five frontier hosted LLMs from Anthropic and OpenAI, each operating as an \"agentic curator\" within a self-contained workspace that supplies the source publication PDF, the same annotation guide used by the original","title":"Frontier LLM-based agents can overcome the ontology curation bottleneck for natural phenotypes","vendor":"arxiv_cs_ai"},"confidence":{"method":"deterministic"},"decision":"POSITIVE","issued_at":"2026-05-29T04:43:58Z","notes":"Spider vendor_press (news) news.vendor_press.v1","object":{"captured_by":"crovia.spider.vendor_press","primary_source_url":"https://arxiv.org/abs/2605.28965"},"predecessors":[],"schema":"crovia.axiom.v1","signature":"ed25519:93e45541519a05764b2974695691079dcf663b23d89f32677afa6a5d6b44011dd3affa2e3d6e0eb19fb330c444c7fc32db6cdd375b26d9138b5bb8ea468f0c0b","signer":"crovia.substrate","subject":{"observed_at":"2026-05-29T04:43:58Z","source_collector":"spider:vendor_press","target_id":"https://arxiv.org/abs/2605.28965"},"tsa":{"authority":"crovia.substrate.bootstrap","rfc3161_token":"{\"kind\":\"crovia.bootstrap.tsa\",\"source_jsonl\":\"/opt/crovia/spider/data/news/vendor_press_v1.jsonl\",\"source_seal_merkle_root\":\"spider_vendor_press_v1\",\"upgrade_path\":\"Sessione H \\u2014 OpenTimestamps weekly anchor\"}"},"zk_mode":"clear","zk_proof":null},"ledger":{"leaf_hash":"0f4d12240bba7328bf048978ef857a98fcbf6b80dd49bc9d8eb4873816929b6e","leaf_index":157650,"ledger_path":"/opt/crovia/substrate/axiom_ledger.jsonl"},"merkle_proof":{"hash_alg":"sha256","leaf_prefix":"0x00","node_prefix":"0x01","odd_leaf_rule":"duplicate_last","path":[{"sibling":"3dbe993dd487498227f66b598f18eff3be55ab50327a8d6cc93b4398952f3f04","side":"right"},{"sibling":"9b9ef80b1ddff3db3c0298b24f49c568bb2d318627a6f519e350f8e36820ac88","side":"left"},{"sibling":"5b22aea3937aea15854d5756ea311d0dfdc2213c02baf7ca229c2df7d76fe8ab","side":"right"},{"sibling":"5d5db581b90d223c2cc94102e6ab6383e4d97f9eb4c3e6899f42a6d610c64a57","side":"right"},{"sibling":"bb9691a4bac0bf4ae76e52675fbd3b05bc40d48fca7c797c7f066a157c7f880a","side":"left"},{"sibling":"043b0b93db31688bb506b27c0bb88b9838dd4a0b5e0340f6fa82e708ed75922b","side":"right"},{"sibling":"f65c4257e1e3e5a8d1432a336a21d8e806501313e0c2888ff215dba80f4c4cfe","side":"left"},{"sibling":"27e5f392a568b11659ecd5aed52502b5e6d88eea7862dffac806a2d7b5a9ef78","side":"left"},{"sibling":"ece7b043912367e6be374d77e09128de032af83a2b87e39b397350dd279ebe83","side":"left"},{"sibling":"39ec45a73732c5ed1abe96972bd3bc32a517083704467dde1c8117578609124d","side":"left"},{"sibling":"68b4895a8015cdde1c1baeaf63a8382cf574ce4d2ad88d596d4217ce2238245e","side":"left"},{"sibling":"0bc831354843fa27f7ba6a4b3080a72fd440b9a76d1bac63429adfbfe6549bca","side":"right"},{"sibling":"995b421824624a8282c7f44e64c64ee35344800f477ae1845b41be14d3fab94c","side":"right"},{"sibling":"66331bac84ca0f8983eb09fac7eaf95af234f1b82680b793eabff4ee25caac40","side":"left"},{"sibling":"35ca36cee447f0ef7064a25d55f59357c66901e31427729c4c1d8b14aa8adb6c","side":"left"},{"sibling":"eef0e8906a749d3470f89beeedc723f37a5737010bbb0dcc7cf91515338e5a3e","side":"right"},{"sibling":"1a07e481a9407d71aad078ce854cdeee362163c887fe10f889b0ecf0b5e749ad","side":"right"},{"sibling":"d841ad93efda0869e5eb97678f348f03f5caab4353e05ff4bf18f47fb945b822","side":"left"}]},"schema":"crovia.axiom_proof.v1","seal":{"first_collector_run_id":"","first_receipt_hash":"","jsonl_path":"/opt/crovia/substrate/axiom_ledger.jsonl","key_id":"430895f101d38164","last_collector_run_id":"","last_receipt_hash":"","leaf_count":158251,"merkle_root":"485e6b31fe60c8beba5b394808c7e4c32448b2ff65c2482c480ca0e2a2eda718","public_key_hex":"cf742e26f75669dc673cb5c0786a1ae23ae8ca19c347317192ce40c28a7ff25c","run_id":"hourly_json_retrofit_20260529T053701Z","schema":"crovia.seal.v1","seal_family_version":"crovia-seal-family/1","seal_kind":"substrate_batch","sealed_at":"2026-05-29T05:37:37Z","sig_algorithm":"ed25519","signature":"bbf9f005201182fce4f9d94c7a9d01a508b56daf7d9611bd73514f5f616bc059d0e5e1f2edfc95716e6fe08ef5fae38b558cbf7f2fd8f9d5dfe4c34a54c83005","signer_version":"1.1.0"},"trust_root":{"key_id":"430895f101d38164","public_key_hex":"cf742e26f75669dc673cb5c0786a1ae23ae8ca19c347317192ce40c28a7ff25c","signature_algorithm":"ed25519","url":"/registry/canon/TRUST_ROOT.md"},"verifier":{"spec":"/registry/canon/AXIOM_RECEIPT_v1.md","url":"/v/axm_ce5419bc9fbd0b385df02f807e6f64b12dc01b0de486c5f638ea81d33be943e3"}}