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Datasets:
Sepideh2027
/
Agent

Tasks:
Text Generation
Tabular Classification
Modalities:
Text
Formats:
csv
Languages:
English
Size:
1M - 10M
Tags:
biomedical
clinvar
genomic-variants
instruction-tuning
text-generation
Libraries:
Datasets
pandas
Polars
License:
Dataset card Data Studio Files
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stringlengths
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765
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88 values
Gene: AP5Z1 | Chr: 7 | Pos: 4781213
Pathogenic/Likely pathogenic
Gene: AP5Z1 | Chr: 7 | Pos: 4787730
Pathogenic
Gene: ZNF592 | Chr: 15 | Pos: 84799209
Uncertain significance
Gene: FOXRED1 | Chr: 11 | Pos: 126275389
Pathogenic
Gene: FOXRED1 | Chr: 11 | Pos: 126277517
Likely pathogenic
Gene: WDR35 | Chr: 2 | Pos: 19989284
Pathogenic
Gene: WDR35 | Chr: 2 | Pos: 19945787
Pathogenic
Gene: WDR35 | Chr: 2 | Pos: 19931375
Pathogenic
Gene: WDR35 | Chr: 2 | Pos: 19933469
Likely pathogenic
Gene: HOGA1 | Chr: 10 | Pos: 97611612
Pathogenic/Likely pathogenic
Gene: HOGA1 | Chr: 10 | Pos: 97611535
Pathogenic
Gene: HOGA1 | Chr: 10 | Pos: 97598852
Pathogenic/Likely pathogenic
Gene: HOGA1 | Chr: 10 | Pos: 97600167
Pathogenic
Gene: HOGA1 | Chr: 10 | Pos: 97584912
Pathogenic/Likely pathogenic
Gene: HOGA1 | Chr: 10 | Pos: 97601925
Pathogenic/Likely pathogenic
Gene: WDPCP | Chr: 2 | Pos: 63492941
Pathogenic
Gene: WDPCP | Chr: 2 | Pos: 63437430
risk factor
Gene: WDPCP | Chr: 2 | Pos: 63487491
risk factor
Gene: TBC1D24 | Chr: 16 | Pos: 2496587
Pathogenic
Gene: TBC1D24 | Chr: 16 | Pos: 2500822
Conflicting classifications of pathogenicity
Gene: TBC1D24 | Chr: 16 | Pos: 2496899
Pathogenic
Gene: XPNPEP3 | Chr: 22 | Pos: 40924482
Pathogenic
Gene: XPNPEP3 | Chr: 22 | Pos: 40909195
Pathogenic
Gene: MTRFR | Chr: 12 | Pos: 123253922
Pathogenic/Likely pathogenic
Gene: MTRFR | Chr: 12 | Pos: 123253884
Pathogenic/Likely pathogenic
Gene: CEP152 | Chr: 15 | Pos: 48793359
Pathogenic/Likely pathogenic
Gene: CEP152 | Chr: 15 | Pos: 48756289
Pathogenic/Likely pathogenic
Gene: OPN1SW | Chr: 7 | Pos: 128775556
Likely benign
Gene: OPN1SW | Chr: 7 | Pos: 128774545
Uncertain significance
Gene: OPN1SW | Chr: 7 | Pos: 128773786
Uncertain significance
Gene: UROD | Chr: 1 | Pos: 45014803
Pathogenic/Likely pathogenic
Gene: UROD | Chr: 1 | Pos: 45014803
Pathogenic
Gene: UROD | Chr: 1 | Pos: 45014071
Pathogenic
Gene: UROD | Chr: 1 | Pos: 45013933
Uncertain significance
Gene: UROD | Chr: 1 | Pos: 45014835
Pathogenic
Gene: UROD | Chr: 1 | Pos: 45013187
Pathogenic
Gene: UROD | Chr: 1 | Pos: 45014996
Conflicting classifications of pathogenicity
Gene: UROD | Chr: 1 | Pos: 45015006
Pathogenic/Likely pathogenic
Gene: UROD | Chr: 1 | Pos: 45013928
Pathogenic/Likely pathogenic
Gene: UROD | Chr: 1 | Pos: 45014017
Pathogenic
Gene: UROD | Chr: 1 | Pos: 45014976
Pathogenic
Gene: UROD | Chr: 1 | Pos: 45015389
Conflicting classifications of pathogenicity
Gene: LIPA | Chr: 10 | Pos: 89225168
Pathogenic
Gene: LIPA | Chr: 10 | Pos: 89223710
Pathogenic
Gene: LIPA | Chr: 10 | Pos: 89225172
Pathogenic
Gene: LIPA | Chr: 10 | Pos: 89222510
Pathogenic
Gene: LIPA | Chr: 10 | Pos: 89245776
Pathogenic
Gene: HPSE2 | Chr: 10 | Pos: 98482733
Pathogenic/Likely pathogenic
Gene: HPSE2 | Chr: 10 | Pos: 98490051
Pathogenic/Likely pathogenic
Gene: HPSE2 | Chr: 10 | Pos: 99235561
Pathogenic
Gene: HPSE2 | Chr: 10 | Pos: 98490103
Pathogenic
Gene: HPSE2 | Chr: 10 | Pos: 99144391
Pathogenic/Likely pathogenic
Gene: HPSE2 | Chr: 10 | Pos: 99235745
Pathogenic
Gene: ASAH1 | Chr: 8 | Pos: 18061724
Pathogenic
Gene: ASAH1 | Chr: 8 | Pos: 18064501
Likely pathogenic
Gene: ASAH1 | Chr: 8 | Pos: 18075559
Pathogenic/Likely pathogenic
Gene: ASAH1 | Chr: 8 | Pos: 18059424
Pathogenic
Gene: ASAH1 | Chr: 8 | Pos: 18062383
Pathogenic
Gene: TCN2 | Chr: 22 | Pos: 30615771
Pathogenic
Gene: TCN2 | Chr: 22 | Pos: 30615623
Benign
Gene: TCN2 | Chr: 22 | Pos: 30613044
Pathogenic
Gene: TCN2 | Chr: 22 | Pos: 30616090
Pathogenic
Gene: TCN2 | Chr: 22 | Pos: 30615125
Pathogenic
Gene: MIR2861 | Chr: 9 | Pos: 127785950
association
Gene: TMEM127 | Chr: 2 | Pos: 96254117
Pathogenic
Gene: TMEM127 | Chr: 2 | Pos: 96254050
Pathogenic/Likely pathogenic
Gene: TMEM127 | Chr: 2 | Pos: 96254998
Pathogenic/Likely pathogenic
Gene: TMEM127 | Chr: 2 | Pos: 96265232
Likely pathogenic; risk factor
Gene: POMP | Chr: 13 | Pos: 28659089
Pathogenic
Gene: TPRN | Chr: 9 | Pos: 137199473
Pathogenic/Likely pathogenic
Gene: TPRN | Chr: 9 | Pos: 137199285
Pathogenic
Gene: TPRN | Chr: 9 | Pos: 137200474
Pathogenic
Gene: TPRN | Chr: 9 | Pos: 137200477
Pathogenic
Gene: TPRN | Chr: 9 | Pos: 137199182
Pathogenic
Gene: OAT | Chr: 10 | Pos: 124412169
Pathogenic
Gene: OAT | Chr: 10 | Pos: 124412013
Pathogenic
Gene: OAT | Chr: 10 | Pos: 124405532
Pathogenic
Gene: OAT | Chr: 10 | Pos: 124398076
Pathogenic/Likely pathogenic
Gene: OAT | Chr: 10 | Pos: 124412009
Pathogenic
Gene: OAT | Chr: 10 | Pos: 124408887
Likely pathogenic
Gene: OAT | Chr: 10 | Pos: 124408601
Likely pathogenic
Gene: OAT | Chr: 10 | Pos: 124405545
Pathogenic/Likely pathogenic
Gene: OAT | Chr: 10 | Pos: 124403019
Pathogenic
Gene: OAT | Chr: 10 | Pos: 124403015
Pathogenic/Likely pathogenic
Gene: OAT | Chr: 10 | Pos: 124398057
Pathogenic
Gene: OAT | Chr: 10 | Pos: 124398012
Pathogenic/Likely pathogenic
Gene: OAT | Chr: 10 | Pos: 124397951
Benign
Gene: OAT | Chr: 10 | Pos: 124400875
Likely pathogenic
Gene: OAT | Chr: 10 | Pos: 124403835
Pathogenic
Gene: OAT | Chr: 10 | Pos: 124400865
Benign
Gene: OAT | Chr: 10 | Pos: 124401746
Pathogenic/Likely pathogenic
Gene: OAT | Chr: 10 | Pos: 124412010
Conflicting classifications of pathogenicity
Gene: OAT | Chr: 10 | Pos: 124401785
Pathogenic
Gene: OAT | Chr: 10 | Pos: 124408633
Pathogenic
Gene: OAT | Chr: 10 | Pos: 124405534
Pathogenic
Gene: OAT | Chr: 10 | Pos: 124403847
Pathogenic/Likely pathogenic
Gene: OAT | Chr: 10 | Pos: 124403820
Pathogenic
Gene: OAT | Chr: 10 | Pos: 124400941
Pathogenic/Likely pathogenic
Gene: OAT | Chr: 10 | Pos: 124398090
Pathogenic/Likely pathogenic
Gene: OAT | Chr: 10 | Pos: 124398082
Uncertain significance
End of preview. Expand in Data Studio

Year: 2025
License: MIT
Author: Sepideh Moafi

PathogenAgentAI Instruction Dataset

Dataset Description

A ClinVar-derived dataset developed as part of the PathogenAgentAI research software project. The dataset is released in two parallel formats:

  • Tabular version (train.csv, valid.csv, test.csv) — structured genomic-variant data for classical ML and analysis.
  • BioGPT instruction version (biogpt_train.csv, biogpt_valid.csv, biogpt_test.csv) — instruction-style data for fine-tuning biomedical language models.

Dataset Structure

Splits

Split Tabular file Instruction file
Train train.csv biogpt_train.csv
Validation valid.csv biogpt_valid.csv
Test test.csv biogpt_test.csv

Tabular Fields

  • GeneSymbol (string): Gene symbol (e.g., AP5Z1, ZNF592)
  • ClinicalSignificance (string): Clinical significance (e.g., Pathogenic, Likely pathogenic, Uncertain significance)
  • Assembly (string): Genome assembly (e.g., GRCh38)
  • Chromosome (string): Chromosome number
  • Start (int64): Variant start position

Instruction Fields

The biogpt_*.csv files are formatted for instruction tuning of biomedical language models (e.g., BioGPT), derived from the same ClinVar source data.

Source Data

Derived from ClinVar, a publicly available archive of reports of the relationships among human variations and phenotypes.

Intended Use

  • Fine-tuning biomedical language models (BioGPT and similar)
  • Research on genomic variant interpretation
  • Classical ML on structured variant data
  • Reproducible biomedical AI experiments

Not intended for clinical diagnosis, treatment decisions, or direct clinical use.

Licensing

Released under the MIT License.

Citation

If you use this dataset in research, please cite:

BioGPT-ClinVar: Parameter-Efficient Fine-Tuning of a Biomedical Foundation Model.
Research Square, 2026. DOI: 10.21203/rs.3.rs-10196893/v1

Contact

Sepideh Moafi
GitHub: AIResearcher20
Hugging Face: Sepideh2027
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