| { |
| "@context": { |
| "@language": "en", |
| "@vocab": "https://schema.org/", |
| "citeAs": "cr:citeAs", |
| "column": "cr:column", |
| "conformsTo": "dct:conformsTo", |
| "cr": "http://mlcommons.org/croissant/", |
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| "@id": "cr:data", |
| "@type": "@json" |
| }, |
| "dataType": { |
| "@id": "cr:dataType", |
| "@type": "@vocab" |
| }, |
| "dct": "http://purl.org/dc/terms/", |
| "equivalentProperty": "cr:equivalentProperty", |
| "examples": "cr:examples", |
| "extract": "cr:extract", |
| "field": "cr:field", |
| "fileObject": "cr:fileObject", |
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| "fileSet": "cr:fileSet", |
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| "key": "cr:key", |
| "md5": "cr:md5", |
| "parentField": "cr:parentField", |
| "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": [ |
| { |
| "@type": "cr:FileObject", |
| "@id": "corpus-jsonl", |
| "name": "corpus.jsonl", |
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| "@id": "pmc-license-manifest-jsonl", |
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| "@id": "hidden-ground-truth-jsonl", |
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| "@id": "hidden-go-terms-json", |
| "name": "hidden_go_terms.json", |
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| "@id": "go-basic-obo", |
| "name": "ontologies/go-basic.obo", |
| "contentUrl": "ontologies/go-basic.obo", |
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| "@id": "fly-anatomy-obo", |
| "name": "ontologies/fly_anatomy.obo", |
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| "recordSet": [ |
| { |
| "@type": "cr:RecordSet", |
| "@id": "corpus-records", |
| "name": "Literature corpus records", |
| "field": [ |
| { |
| "@type": "cr:Field", |
| "@id": "corpus-records/pmcid", |
| "name": "pmcid", |
| "dataType": "sc:Text", |
| "source": { |
| "fileObject": { |
| "@id": "corpus-jsonl" |
| }, |
| "extract": { |
| "jsonPath": "$.pmcid" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "corpus-records/title", |
| "name": "title", |
| "dataType": "sc:Text", |
| "source": { |
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| "@id": "corpus-jsonl" |
| }, |
| "extract": { |
| "jsonPath": "$.title" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "corpus-records/abstract", |
| "name": "abstract", |
| "dataType": "sc:Text", |
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| "jsonPath": "$.abstract" |
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| "@id": "corpus-records/sections", |
| "name": "sections", |
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| }, |
| "extract": { |
| "jsonPath": "$.sections" |
| } |
| } |
| } |
| ] |
| }, |
| { |
| "@type": "cr:RecordSet", |
| "@id": "benchmark-records", |
| "name": "Benchmark gene records with verified ground truth", |
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| { |
| "@type": "cr:Field", |
| "@id": "benchmark-records/gene_id", |
| "name": "gene_id", |
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| "extract": { |
| "jsonPath": "$.gene_id" |
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| "name": "gene_symbol", |
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| "extract": { |
| "jsonPath": "$.gene_symbol" |
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| { |
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| "name": "pmcids", |
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| "@id": "benchmark-jsonl" |
| }, |
| "extract": { |
| "jsonPath": "$.pmcids" |
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| } |
| }, |
| { |
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| "name": "task1_function", |
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| }, |
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| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark-records/task2_expression", |
| "name": "task2_expression", |
| "dataType": "sc:Text", |
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| "@id": "benchmark-jsonl" |
| }, |
| "extract": { |
| "jsonPath": "$.task2_expression" |
| } |
| } |
| }, |
| { |
| "@type": "cr:Field", |
| "@id": "benchmark-records/task3_synonyms", |
| "name": "task3_synonyms", |
| "dataType": "sc:Text", |
| "source": { |
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| }, |
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| "jsonPath": "$.task3_synonyms" |
| } |
| } |
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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." |
| } |
|
|
