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pixi.toml ADDED
@@ -0,0 +1,12 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ [project]
2
+ authors = ["Shlok Natarajan <shlok.natarajan@gmail.com>"]
3
+ channels = ["conda-forge"]
4
+ name = "autogkb-dataset"
5
+ platforms = ["osx-arm64"]
6
+ version = "0.1.0"
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+
8
+ [tasks]
9
+
10
+ [dependencies]
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+ pandas = ">=2.2.3,<3"
12
+ datasets = ">=3.6.0,<4"
variant_drug_benchmark.py CHANGED
@@ -10,16 +10,16 @@ import datasets
10
 
11
 
12
  _CITATION = """\
13
- @misc{variant_drug_benchmark_2024,
14
- title={Variant-Drug Annotation Benchmark},
15
- author={AutoGKB Team},
16
- year={2024},
17
  note={A benchmark for pharmacogenomic variant-drug annotation extraction from scientific literature}
18
  }
19
  """
20
 
21
  _DESCRIPTION = """\
22
- The Variant-Drug Annotation Benchmark evaluates models' ability to extract pharmacogenomic variant-drug associations from scientific literature.
23
 
24
  This dataset contains 4,516 annotations across 1,431 papers, covering genetic variants, drugs, phenotype categories, and association details. Each annotation includes 22 fields ranging from core information (variant, gene, drug, PMID) to detailed phenotype and association data.
25
 
@@ -40,8 +40,8 @@ _LICENSE = "Apache-2.0"
40
  _URLS = {}
41
 
42
 
43
- class VariantDrugBenchmark(datasets.GeneratorBasedBuilder):
44
- """Variant-Drug Annotation Benchmark dataset."""
45
 
46
  VERSION = datasets.Version("1.0.0")
47
 
@@ -49,7 +49,7 @@ class VariantDrugBenchmark(datasets.GeneratorBasedBuilder):
49
  datasets.BuilderConfig(
50
  name="default",
51
  version=VERSION,
52
- description="The full Variant-Drug Annotation Benchmark dataset",
53
  ),
54
  ]
55
 
 
10
 
11
 
12
  _CITATION = """\
13
+ @misc{autogkb_annotation_benchmark_2025,
14
+ title={AutoGKB Annotation Benchmark},
15
+ author={Shlok Natarajan},
16
+ year={2025},
17
  note={A benchmark for pharmacogenomic variant-drug annotation extraction from scientific literature}
18
  }
19
  """
20
 
21
  _DESCRIPTION = """\
22
+ The AutoGKB Annotation Benchmark evaluates models' ability to extract pharmacogenomic variant-drug associations from scientific literature.
23
 
24
  This dataset contains 4,516 annotations across 1,431 papers, covering genetic variants, drugs, phenotype categories, and association details. Each annotation includes 22 fields ranging from core information (variant, gene, drug, PMID) to detailed phenotype and association data.
25
 
 
40
  _URLS = {}
41
 
42
 
43
+ class AutoGKBAnnotationBenchmark(datasets.GeneratorBasedBuilder):
44
+ """AutoGKB Annotation Benchmark dataset."""
45
 
46
  VERSION = datasets.Version("1.0.0")
47
 
 
49
  datasets.BuilderConfig(
50
  name="default",
51
  version=VERSION,
52
+ description="The full AutoGKB Annotation Benchmark dataset",
53
  ),
54
  ]
55