{
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    "dct": "http://purl.org/dc/terms/",
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    "fileSet": "cr:fileSet",
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    "md5": "cr:md5",
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    "path": "cr:path",
    "recordSet": "cr:recordSet",
    "references": "cr:references",
    "regex": "cr:regex",
    "repeated": "cr:repeated",
    "replace": "cr:replace",
    "samplingRate": "cr:samplingRate",
    "sc": "https://schema.org/",
    "separator": "cr:separator",
    "source": "cr:source",
    "subField": "cr:subField",
    "transform": "cr:transform",
    "rai": "http://mlcommons.org/croissant/RAI/",
    "prov": "http://www.w3.org/ns/prov#"
  },
  "@type": "sc:Dataset",
  "name": "FlyAOC: Agentic Ontology Curation Benchmark",
  "description": "A benchmark for evaluating AI agents on end-to-end ontology curation from a corpus of Drosophila full-text scientific articles.",
  "url": "https://huggingface.co/datasets/anonymous-042/flyaoc",
  "sameAs": "https://github.com/anonymous-flyaoc/flyaoc",
  "citeAs": "FlyAOC: Agentic Ontology Curation Benchmark. NeurIPS 2026 Evaluations and Datasets Track submission.",
  "datePublished": "2026-04-30",
  "version": "1.0.0",
  "conformsTo": "http://mlcommons.org/croissant/1.1",
  "license": [
    "https://creativecommons.org/licenses/by/4.0/",
    "Article-level PMC-OA licenses vary; see pmc_license_manifest.jsonl."
  ],
  "distribution": [
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      "@id": "corpus-jsonl",
      "name": "corpus.jsonl",
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      "@id": "hidden-ground-truth-jsonl",
      "name": "ground_truth_hidden.jsonl",
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      "@id": "fly-anatomy-obo",
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      "@id": "fly-development-obo",
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      "@type": "cr:RecordSet",
      "@id": "corpus-records",
      "name": "Literature corpus records",
      "field": [
        {
          "@type": "cr:Field",
          "@id": "corpus-records/pmcid",
          "name": "pmcid",
          "dataType": "sc:Text",
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            "extract": {
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          "@id": "corpus-records/title",
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            },
            "extract": {
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            "extract": {
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          }
        },
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          "@id": "corpus-records/sections",
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          "source": {
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            },
            "extract": {
              "jsonPath": "$.sections"
            }
          }
        }
      ]
    },
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      "@type": "cr:RecordSet",
      "@id": "benchmark-records",
      "name": "Benchmark gene records with verified ground truth",
      "field": [
        {
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          "@id": "benchmark-records/gene_id",
          "name": "gene_id",
          "dataType": "sc:Text",
          "source": {
            "fileObject": {
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            },
            "extract": {
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        },
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          "name": "gene_symbol",
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            "extract": {
              "jsonPath": "$.gene_symbol"
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        },
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        },
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          "@id": "benchmark-records/pmcids",
          "name": "pmcids",
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          "source": {
            "fileObject": {
              "@id": "benchmark-jsonl"
            },
            "extract": {
              "jsonPath": "$.pmcids"
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          }
        },
        {
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          "@id": "benchmark-records/task1_function",
          "name": "task1_function",
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            },
            "extract": {
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        },
        {
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        },
        {
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            "extract": {
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  ],
  "rai:dataLimitations": "FlyAOC covers 100 well-studied Drosophila genes and PMC-OA full-text literature. It does not cover all genes, all organisms, paywalled papers, non-English literature, unpublished evidence, or every valid biological annotation.",
  "rai:dataBiases": "The corpus reflects publication and open-access biases, with overrepresentation of English-language, well-studied, and PMC-indexed literature. FlyBase-derived labels reflect expert curation priorities and may lag recent publications.",
  "rai:personalSensitiveInformation": "The dataset is composed of scientific articles and biological database annotations. It is not designed to include human-subject records or private personal information, though source articles may contain public author names and affiliations.",
  "rai:dataUseCases": "The dataset is intended to evaluate retrieval-augmented and agentic systems for ontology-grounded literature curation. It is not intended as a stand-alone source of validated biological annotations for production databases without expert review.",
  "rai:dataSocialImpact": "The dataset can support research on curator-assistive systems for biological databases. Risks include over-trusting automated annotations or deploying systems without professional curator oversight.",
  "rai:hasSyntheticData": false,
  "prov:wasDerivedFrom": [
    "https://www.ncbi.nlm.nih.gov/pmc/tools/openftlist/",
    "https://flybase.org/",
    "http://geneontology.org/",
    "https://obofoundry.org/"
  ],
  "prov:wasGeneratedBy": "PMC-OA articles were retrieved through the BioC-PMC API and converted to JSONL. FlyBase release FB2025_04 annotations were processed into three benchmark tasks, annotated with corpus-grounding labels, and merged with gene summaries and gene-to-paper mappings into benchmark.jsonl. Gene Ontology and FlyBase ontology source files were included to fix the controlled vocabularies used by the benchmark tools and semantic evaluation. A hidden-term variant marks selected GO labels for specificity-gap evaluation."
}