Add FlyAOC dataset package

.gitattributes

@@ -58,3 +58,6 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+corpus.jsonl filter=lfs diff=lfs merge=lfs -text
+ontologies/fly_anatomy.obo filter=lfs diff=lfs merge=lfs -text
+ontologies/go-basic.obo filter=lfs diff=lfs merge=lfs -text

README.md

@@ -0,0 +1,112 @@
+---
+license: other
+pretty_name: FlyAOC
+task_categories:
+  - text-generation
+  - question-answering
+  - text-retrieval
+language:
+  - en
+tags:
+  - biology
+  - drosophila
+  - genetics
+  - scientific-literature
+  - ontology-curation
+  - benchmark
+size_categories:
+  - 10K<n<100K
+---
+
+# FlyAOC: Agentic Ontology Curation Benchmark
+
+FlyAOC is a benchmark for evaluating AI agents on end-to-end ontology curation from scientific literature. Given a *Drosophila melanogaster* gene symbol, systems search a corpus of full-text papers and produce structured annotations for gene function, expression, and synonyms.
+
+This anonymous review package contains the benchmark inputs and labels, not model prediction dumps.
+
+## Files
+
+| File | Description |
+|---|---|
+| `corpus.jsonl` | 16,898 full-text PMC-OA articles converted from BioC JSON. |
+| `pmc_license_manifest.jsonl` | Per-record provenance and license metadata extracted from the BioC-PMC source files. |
+| `benchmark.jsonl` | The 100 benchmark genes, with FlyBase IDs, symbols, Gene Snapshot summaries, PMCID retrieval sets, and canonical verified labels for all three tasks. |
+| `ground_truth_hidden.jsonl` | Hidden-term benchmark variant labels. |
+| `hidden_go_terms.json` | The GO terms hidden for the specificity-gap setting. |
+| `ontologies/go-basic.obo` | Gene Ontology source used for Task 1 term lookup and semantic evaluation. |
+| `ontologies/fly_anatomy.obo` | FlyBase anatomy ontology source used for Task 2 anatomy lookup and semantic evaluation. |
+| `ontologies/fly_development.obo` | FlyBase developmental stage ontology source used for Task 2 stage lookup and semantic evaluation. |
+| `croissant.json` | Croissant metadata with core and minimal Responsible AI fields. |
+
+## Data Schema
+
+Each `corpus.jsonl` record contains:
+
+- `pmcid`: PubMed Central identifier.
+- `title`: article title.
+- `abstract`: article abstract.
+- `sections`: mapping from section type to paragraphs, using section keys such as `INTRO`, `METHODS`, `RESULTS`, `DISCUSS`, and `CONCL`.
+
+Each `benchmark.jsonl` record contains one gene:
+
+- `gene_id`, `gene_symbol`, `summary`, `pmcids`
+- `task1_function`: Gene Ontology annotations with GO ID, qualifier, aspect, evidence reference, and corpus-grounding fields.
+- `task2_expression`: expression annotations with anatomy/stage ontology IDs, assay metadata, evidence reference, and corpus-grounding fields.
+- `task3_synonyms`: full-name and symbol synonyms with corpus-grounding fields.
+
+## Intended Use
+
+FlyAOC is intended for evaluating systems that retrieve and synthesize structured biological annotations from a large literature corpus. The primary use case is benchmark evaluation of curation agents under controlled retrieval budgets. The dataset is not intended to train production biomedical systems without additional validation by domain experts.
+
+## Provenance and Annotation
+
+The literature corpus was retrieved from the PubMed Central Open Access subset via the BioC-PMC API. Benchmark labels are derived from FlyBase release FB2025_04 and then annotated with corpus-grounding labels that indicate whether the supporting source is present in the provided corpus. The included ontology files define the controlled vocabularies used by the benchmark tools and semantic evaluation. The hidden-term variant removes selected GO terms from ontology search to test whether systems can describe missing concepts when no suitable ontology term is available.
+
+## License and Access
+
+This package has mixed provenance and should not be treated as having a single blanket license.
+
+- Literature records come from the PubMed Central Open Access subset. Article licenses vary by paper; see `pmc_license_manifest.jsonl` for per-record license metadata.
+- FlyBase-derived benchmark labels and FlyBase ontology files are based on FlyBase data released under CC-BY 4.0.
+- Gene Ontology files are released under CC-BY 4.0.
+- Users are responsible for following the terms associated with each source record. Users with stricter licensing requirements may use the PMCID manifest to re-fetch source articles from PMC directly.
+
+## Responsible AI Notes
+
+### Limitations
+
+The benchmark covers 100 well-studied *Drosophila* genes and open-access literature available through PMC-OA. It does not represent all genes, all organisms, non-English literature, paywalled papers, unpublished curation evidence, or all valid biological annotations.
+
+### Biases
+
+The corpus reflects publication and open-access biases in the scientific record. Well-studied genes, English-language publications, and journals indexed in PMC-OA are overrepresented. FlyBase labels reflect expert curation priorities and may lag newer literature.
+
+### Sensitive Information
+
+The dataset contains scientific articles and biological database annotations. It is not designed to contain human-subject records, demographic attributes, or private personal information. Some source articles may include author names, affiliations, and acknowledgments as part of the public scholarly record.
+
+### Social Impact
+
+The benchmark may help improve tools that assist biological database curation and scientific literature review. Misuse risks include over-trusting automated annotations or deploying systems without expert review. FlyAOC should be used as an evaluation resource, not as a substitute for professional biological curation.
+
+### Synthetic Data
+
+The corpus and benchmark labels are not synthetic. Model-generated predictions are not included in this dataset package.
+
+## Loading
+
+```python
+from datasets import load_dataset
+
+corpus = load_dataset("json", data_files="corpus.jsonl")["train"]
+benchmark = load_dataset("json", data_files="benchmark.jsonl")["train"]
+```
+
+For review, the intended hosted dataset path is:
+
+```python
+from datasets import load_dataset
+
+corpus = load_dataset("anonymous-042/flyaoc", data_files="corpus.jsonl")["train"]
+benchmark = load_dataset("anonymous-042/flyaoc", data_files="benchmark.jsonl")["train"]
+```

corpus.jsonl

@@ -0,0 +1,3 @@
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+oid sha256:8b7236a3dba5578b3f8f29c06d42bd4a8d36b1b8985324b257d64102698af8d8
+size 660303756

croissant.json

@@ -0,0 +1,309 @@
+{
+  "@context": {
+    "@language": "en",
+    "@vocab": "https://schema.org/",
+    "citeAs": "cr:citeAs",
+    "column": "cr:column",
+    "conformsTo": "dct:conformsTo",
+    "cr": "http://mlcommons.org/croissant/",
+    "data": {
+      "@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",
+    "fileProperty": "cr:fileProperty",
+    "fileSet": "cr:fileSet",
+    "format": "cr:format",
+    "includes": "cr:includes",
+    "isLiveDataset": "cr:isLiveDataset",
+    "jsonPath": "cr:jsonPath",
+    "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",
+      "contentUrl": "corpus.jsonl",
+      "encodingFormat": "application/jsonlines",
+      "sha256": "8b7236a3dba5578b3f8f29c06d42bd4a8d36b1b8985324b257d64102698af8d8"
+    },
+    {
+      "@type": "cr:FileObject",
+      "@id": "pmc-license-manifest-jsonl",
+      "name": "pmc_license_manifest.jsonl",
+      "contentUrl": "pmc_license_manifest.jsonl",
+      "encodingFormat": "application/jsonlines",
+      "sha256": "a0e6daca2986fe7ca3eef30bec5bce9225fc70f81fde36493c180fccf036cc9d"
+    },
+    {
+      "@type": "cr:FileObject",
+      "@id": "benchmark-jsonl",
+      "name": "benchmark.jsonl",
+      "contentUrl": "benchmark.jsonl",
+      "encodingFormat": "application/jsonlines",
+      "sha256": "a27e5f2dd9f65678de01366649c2d657195704a9ebc42eea020c44a84f9e2c9a"
+    },
+    {
+      "@type": "cr:FileObject",
+      "@id": "hidden-ground-truth-jsonl",
+      "name": "ground_truth_hidden.jsonl",
+      "contentUrl": "ground_truth_hidden.jsonl",
+      "encodingFormat": "application/jsonlines",
+      "sha256": "576395b1aafa47cc499ca5a0e4c82dfe9d567f0dac8d795f022b820b222cbab4"
+    },
+    {
+      "@type": "cr:FileObject",
+      "@id": "hidden-go-terms-json",
+      "name": "hidden_go_terms.json",
+      "contentUrl": "hidden_go_terms.json",
+      "encodingFormat": "application/json",
+      "sha256": "26a4ead741351b96303d81316235a8edd775565a757e8f64ae0b39a0efa7d936"
+    },
+    {
+      "@type": "cr:FileObject",
+      "@id": "go-basic-obo",
+      "name": "ontologies/go-basic.obo",
+      "contentUrl": "ontologies/go-basic.obo",
+      "encodingFormat": "text/obo",
+      "sha256": "4e3ce039a6ad3d45e2752097625330152cc8ae97d35d824c7fcb0735b45d0fc3"
+    },
+    {
+      "@type": "cr:FileObject",
+      "@id": "fly-anatomy-obo",
+      "name": "ontologies/fly_anatomy.obo",
+      "contentUrl": "ontologies/fly_anatomy.obo",
+      "encodingFormat": "text/obo",
+      "sha256": "50cbbc694414f765b2cae8b27984fc96e0627774e2e1e55e02197259e292f2be"
+    },
+    {
+      "@type": "cr:FileObject",
+      "@id": "fly-development-obo",
+      "name": "ontologies/fly_development.obo",
+      "contentUrl": "ontologies/fly_development.obo",
+      "encodingFormat": "text/obo",
+      "sha256": "6f9803cc02a3bf8fe843cdc66d8af08de3cd6f71f87337b9acbaaa6f085fa686"
+    }
+  ],
+  "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": "$.pmcid"
+            }
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "corpus-records/title",
+          "name": "title",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "corpus-jsonl"
+            },
+            "extract": {
+              "jsonPath": "$.title"
+            }
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "corpus-records/abstract",
+          "name": "abstract",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "corpus-jsonl"
+            },
+            "extract": {
+              "jsonPath": "$.abstract"
+            }
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "corpus-records/sections",
+          "name": "sections",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "corpus-jsonl"
+            },
+            "extract": {
+              "jsonPath": "$.sections"
+            }
+          }
+        }
+      ]
+    },
+    {
+      "@type": "cr:RecordSet",
+      "@id": "benchmark-records",
+      "name": "Benchmark gene records with verified ground truth",
+      "field": [
+        {
+          "@type": "cr:Field",
+          "@id": "benchmark-records/gene_id",
+          "name": "gene_id",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "benchmark-jsonl"
+            },
+            "extract": {
+              "jsonPath": "$.gene_id"
+            }
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "benchmark-records/gene_symbol",
+          "name": "gene_symbol",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "benchmark-jsonl"
+            },
+            "extract": {
+              "jsonPath": "$.gene_symbol"
+            }
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "benchmark-records/summary",
+          "name": "summary",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "benchmark-jsonl"
+            },
+            "extract": {
+              "jsonPath": "$.summary"
+            }
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "benchmark-records/pmcids",
+          "name": "pmcids",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "benchmark-jsonl"
+            },
+            "extract": {
+              "jsonPath": "$.pmcids"
+            }
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "benchmark-records/task1_function",
+          "name": "task1_function",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "benchmark-jsonl"
+            },
+            "extract": {
+              "jsonPath": "$.task1_function"
+            }
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "benchmark-records/task2_expression",
+          "name": "task2_expression",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "benchmark-jsonl"
+            },
+            "extract": {
+              "jsonPath": "$.task2_expression"
+            }
+          }
+        },
+        {
+          "@type": "cr:Field",
+          "@id": "benchmark-records/task3_synonyms",
+          "name": "task3_synonyms",
+          "dataType": "sc:Text",
+          "source": {
+            "fileObject": {
+              "@id": "benchmark-jsonl"
+            },
+            "extract": {
+              "jsonPath": "$.task3_synonyms"
+            }
+          }
+        }
+      ]
+    }
+  ],
+  "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."
+}

hidden_go_terms.json

@@ -0,0 +1,270 @@
+{
+  "hidden_terms": [
+    "GO:0000022",
+    "GO:0000070",
+    "GO:0000139",
+    "GO:0000159",
+    "GO:0000242",
+    "GO:0000381",
+    "GO:0000776",
+    "GO:0000779",
+    "GO:0000794",
+    "GO:0001222",
+    "GO:0001228",
+    "GO:0001580",
+    "GO:0001700",
+    "GO:0001742",
+    "GO:0001745",
+    "GO:0002052",
+    "GO:0003007",
+    "GO:0003726",
+    "GO:0004653",
+    "GO:0004691",
+    "GO:0005031",
+    "GO:0005096",
+    "GO:0005109",
+    "GO:0005525",
+    "GO:0005546",
+    "GO:0005615",
+    "GO:0005635",
+    "GO:0005640",
+    "GO:0005654",
+    "GO:0005700",
+    "GO:0005730",
+    "GO:0005739",
+    "GO:0005759",
+    "GO:0005771",
+    "GO:0005814",
+    "GO:0005834",
+    "GO:0005865",
+    "GO:0005914",
+    "GO:0005925",
+    "GO:0005927",
+    "GO:0007080",
+    "GO:0007098",
+    "GO:0007157",
+    "GO:0007254",
+    "GO:0007265",
+    "GO:0007283",
+    "GO:0007298",
+    "GO:0007300",
+    "GO:0007318",
+    "GO:0007395",
+    "GO:0007508",
+    "GO:0007512",
+    "GO:0007628",
+    "GO:0008335",
+    "GO:0008594",
+    "GO:0015030",
+    "GO:0016028",
+    "GO:0016327",
+    "GO:0016328",
+    "GO:0016528",
+    "GO:0019178",
+    "GO:0030165",
+    "GO:0030576",
+    "GO:0030619",
+    "GO:0030620",
+    "GO:0030621",
+    "GO:0030717",
+    "GO:0030721",
+    "GO:0031005",
+    "GO:0031036",
+    "GO:0031315",
+    "GO:0032226",
+    "GO:0033039",
+    "GO:0035170",
+    "GO:0035186",
+    "GO:0035199",
+    "GO:0036082",
+    "GO:0036098",
+    "GO:0042595",
+    "GO:0042691",
+    "GO:0043395",
+    "GO:0043505",
+    "GO:0045170",
+    "GO:0045199",
+    "GO:0045450",
+    "GO:0045855",
+    "GO:0046012",
+    "GO:0048190",
+    "GO:0048674",
+    "GO:0048846",
+    "GO:0050829",
+    "GO:0051382",
+    "GO:0052576",
+    "GO:0060289",
+    "GO:0060439",
+    "GO:0061176",
+    "GO:0070285",
+    "GO:0070300",
+    "GO:0070732",
+    "GO:0071212",
+    "GO:0071244",
+    "GO:0071276",
+    "GO:0071361",
+    "GO:0071632",
+    "GO:0071889",
+    "GO:0072553",
+    "GO:0090298",
+    "GO:0097150",
+    "GO:0098595",
+    "GO:0102757",
+    "GO:0106036",
+    "GO:0110069",
+    "GO:0110071",
+    "GO:0141009",
+    "GO:1900006",
+    "GO:1900074",
+    "GO:1900075",
+    "GO:1905866",
+    "GO:1990255",
+    "GO:1990474"
+  ],
+  "primary_terms": [
+    "GO:0000022",
+    "GO:0000070",
+    "GO:0000139",
+    "GO:0000159",
+    "GO:0000242",
+    "GO:0000381",
+    "GO:0000776",
+    "GO:0000779",
+    "GO:0000794",
+    "GO:0001222",
+    "GO:0001228",
+    "GO:0001580",
+    "GO:0001700",
+    "GO:0001742",
+    "GO:0001745",
+    "GO:0002052",
+    "GO:0003007",
+    "GO:0003726",
+    "GO:0004653",
+    "GO:0004691",
+    "GO:0005031",
+    "GO:0005096",
+    "GO:0005109",
+    "GO:0005525",
+    "GO:0005546",
+    "GO:0005615",
+    "GO:0005635",
+    "GO:0005640",
+    "GO:0005654",
+    "GO:0005700",
+    "GO:0005730",
+    "GO:0005739",
+    "GO:0005759",
+    "GO:0005771",
+    "GO:0005814",
+    "GO:0005834",
+    "GO:0005865",
+    "GO:0005914",
+    "GO:0005925",
+    "GO:0005927",
+    "GO:0007080",
+    "GO:0007098",
+    "GO:0007157",
+    "GO:0007254",
+    "GO:0007265",
+    "GO:0007283",
+    "GO:0007298",
+    "GO:0007300",
+    "GO:0007318",
+    "GO:0007395",
+    "GO:0007508",
+    "GO:0007512",
+    "GO:0007628",
+    "GO:0008335",
+    "GO:0008594",
+    "GO:0015030",
+    "GO:0016028",
+    "GO:0016327",
+    "GO:0016328",
+    "GO:0016528",
+    "GO:0019178",
+    "GO:0030165",
+    "GO:0030576",
+    "GO:0030619",
+    "GO:0030620",
+    "GO:0030621",
+    "GO:0030717",
+    "GO:0030721",
+    "GO:0031005",
+    "GO:0031036",
+    "GO:0031315",
+    "GO:0032226",
+    "GO:0033039",
+    "GO:0035170",
+    "GO:0035186",
+    "GO:0035199",
+    "GO:0036082",
+    "GO:0036098",
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