Improving data card
Browse files
README.md
CHANGED
@@ -1,3 +1,43 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
---
|
2 |
license: mit
|
3 |
---
|
|
|
1 |
+
# Dataset Description
|
2 |
+
|
3 |
+
|
4 |
+
## Dataset Summary
|
5 |
+
|
6 |
+
This dataset was derived from the Los Alamos National Laboratory HIV sequence (LANL) database.
|
7 |
+
It contains 2,935 HIV V3 loop protein sequences, which can interact with either CCR5 receptors on T-Cells or CXCR4 receptors on macrophages.
|
8 |
+
|
9 |
+
Supported Tasks and Leaderboards: None
|
10 |
+
|
11 |
+
Languages: English
|
12 |
+
|
13 |
+
## Dataset Structure
|
14 |
+
|
15 |
+
### Data Instances
|
16 |
+
Data Instances: Each column represents the protein amino acid sequence of the HIV V3 loop.
|
17 |
+
The ID field indicates the Genbank reference ID for future cross-referencing.
|
18 |
+
There are 2,935 total V3 sequences, with 91% being CCR5 tropic and 23% CXCR4 tropic.
|
19 |
+
Data Fields: ID, sequence, fold, CCR5, CXCR4
|
20 |
+
Data Splits: None
|
21 |
+
|
22 |
+
## Dataset Creation
|
23 |
+
|
24 |
+
Curation Rationale: This dataset was curated to train a model (HIV-BERT-V3) designed to predict whether an HIV V3 loop would be CCR5 or CXCR4 tropic.
|
25 |
+
|
26 |
+
Initial Data Collection and Normalization: Dataset was downloaded and curated on 12/20/2021.
|
27 |
+
|
28 |
+
## Considerations for Using the Data
|
29 |
+
|
30 |
+
Social Impact of Dataset: This dataset can be used to study the mechanism by which HIV V3 loops allow for entry into T-cells and macrophages.
|
31 |
+
|
32 |
+
Discussion of Biases: Due 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.
|
33 |
+
Currently, there was no effort made to balance the performance across these classes.
|
34 |
+
As such, one should consider refinement with additional sequences to perform well on non-B sequences.
|
35 |
+
|
36 |
+
## Additional Information:
|
37 |
+
- Dataset Curators: Will Dampier
|
38 |
+
- Citation Information: TBA
|
39 |
+
|
40 |
+
|
41 |
---
|
42 |
license: mit
|
43 |
---
|