| # Dataset Description | |
| ## Dataset Summary | |
| This dataset was derived from the Los Alamos National Laboratory HIV sequence (LANL) database. | |
| It contains 5,510 unique V3 sequences, each annotated with its corresponding bodysite that it was associated with. | |
| Supported Tasks and Leaderboards: None | |
| Languages: English | |
| ## Dataset Structure | |
| ### Data Instances | |
| Data Instances: Each column represents the protein amino acid sequence of the HIV V3 loop. | |
| The ID field indicates the Genbank reference ID for future cross-referencing. | |
| There are 2,935 total V3 sequences, with 91% being CCR5 tropic and 23% CXCR4 tropic. | |
| Data Fields: ID, sequence, fold, periphery-tcell, periphery-monocyte, CNS, lung, breast-milk, gastric, male-genitals, female-genitals, umbilical-cord, organ | |
| Data Splits: None | |
| ## Dataset Creation | |
| Curation Rationale: | |
| Initial Data Collection and Normalization: Dataset was downloaded and curated on 12/20/2021. | |
| ## Considerations for Using the Data | |
| Social Impact of Dataset: This dataset can be used to study the mechanism by which HIV V3 loops allow for study of HIV compartmentalization. | |
| Discussion of Biases: DDue to the sampling nature of this database, it is predominantly composed of subtype B sequences from North America and Europe with only minor contributions of Subtype C, A, and D. | |
| Currently, there was no effort made to balance the performance across these classes. | |
| As such, one should consider refinement with additional sequences to perform well on non-B sequences. | |
| Additionally, this dataset is highly biased to peripheral T-cells. | |
| ## Additional Information: | |
| - Dataset Curators: Will Dampier | |
| - Citation Information: TBA | |
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| license: mit | |
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