---
pretty_name: Enterococcus clean-v2 plasmid segment dataset
tags:
- biology
- genomics
- plasmid
- enterococcus
- prokbert
language:
- en
configs:
- config_name: enterococcus_clean_v2_host_assemblies
  data_files:
  - split: train
    path: data/enterococcus_clean_v2_host_assemblies/train-*.parquet
- config_name: enterococcus_clean_v2_host_contigs
  data_files:
  - split: train
    path: data/enterococcus_clean_v2_host_contigs/train-*.parquet
- config_name: enterococcus_clean_v2_plasmid_to_assembly_links
  data_files:
  - split: train
    path: data/enterococcus_clean_v2_plasmid_to_assembly_links/train-*.parquet
- config_name: enterococcus_clean_v2_plasmids
  data_files:
  - split: train
    path: data/enterococcus_clean_v2_plasmids/train-*.parquet
- config_name: enterococcus_clean_v2_segments
  data_files:
  - split: train
    path: data/enterococcus_clean_v2_segments/train-*.parquet
---

<!-- BEGIN ENTEROCOCCUS_CLEAN_V2_SEGMENT_DATASET -->
# Enterococcus Clean-v2 Segment Dataset

This dataset contains the Enterococcus clean-v2 NR plasmid training segments and their sampled host candidate segments. Problematic host segments are not dropped from the canonical export; they are retained and tagged.

## Configs

| config | split | rows | has_sequence |
| --- | --- | --- | --- |
| enterococcus_clean_v2_host_assemblies | train | 1497 | False |
| enterococcus_clean_v2_host_contigs | train | 4530 | False |
| enterococcus_clean_v2_plasmid_to_assembly_links | train | 7916 | False |
| enterococcus_clean_v2_plasmids | train | 2519 | False |
| enterococcus_clean_v2_segments | train | 910900 | True |

Only `enterococcus_clean_v2_segments` contains the nucleotide segment sequence column.

## Counts

| metric | value |
| --- | ---: |
| plasmid segment rows | 182180 |
| host candidate rows | 728720 |
| total canonical rows | 910900 |
| host rows flagged by plasmid overlap | 27417 |
| current clean-training eligible rows | 883483 |
| unique source sequence IDs | 5133 |
| selected Enterococcus clean-v2 NR plasmids | 2519 |
| host assemblies with usable non-plasmid contigs | 1497 |

## Segment Flags

- `segment_id`: unique integer primary key, contiguous from `0`.
- `sequence_id`: source-sequence grouping ID, contiguous from `0`; segments from the same plasmid or host source contig share one value.
- `labels`: `1` for plasmid segments, `0` for host segments.
- `training_eligible_current_clean`: current recommended training filter.
- `filtered_by_plasmid`: host segment has a likely plasmid-overlap minimap2 hit.
- `is_problematic_segment`: currently equivalent to a host segment flagged by plasmid overlap.
- `problematic_reasons`: text reason for problematic rows, currently `host_plasmid_overlap`.

## Loading

```python
from datasets import load_dataset

segments = load_dataset("neuralbioinfo/enterococcus-plasmid-training", "enterococcus_clean_v2_segments", split="train")
clean = segments.filter(lambda row: row["training_eligible_current_clean"])
flagged_hosts = segments.filter(lambda row: row["source_type"] == "host" and row["filtered_by_plasmid"])
```

## Provenance

- Source clean-v2 plasmid DB: `clean_v2_len2k_4mb_nochrom_broadhq20`
- Taxonomic scope: Enterococcus genus taxid `1350`
- Segment length: `4000`
- Plasmid coverage: `2.0`
- Host candidate ratio: `4x`
- Host-overlap filter: minimap2 against selected Enterococcus clean-v2 NR plasmids.

Detailed JSON reports are stored under `reports/`.
<!-- END ENTEROCOCCUS_CLEAN_V2_SEGMENT_DATASET -->