Duplicate from AGI-FBHC/NL2Protein

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+nl_to_seq_1.jsonl filter=lfs diff=lfs merge=lfs -text
+NL2Protein.jsonl filter=lfs diff=lfs merge=lfs -text
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+NL2Protein.csv filter=lfs diff=lfs merge=lfs -text
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NL2Protein.csv

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README.md

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+---
+language:
+- en
+tags:
+- protein
+- bioinformatics
+- protein sequence
+- protein function
+- enzyme
+- uniprot
+- sequence-to-text
+- protein annotation
+- biological process
+- molecular function
+- cellular component
+configs:
+- config_name: default
+  description: Protein sequences with functional descriptions and annotations.
+  data_files:
+  - split: train
+    path: NL2Protein.csv
+  features:
+  - name: ID
+    dtype: string
+  - name: Text
+    dtype: string
+  - name: Protein
+    dtype: string
+  - name: Species
+    dtype: string
+  - name: Family
+    dtype: string
+  viewer:
+    type: table
+    rows_per_page: 10
+size_categories:
+- 100K<n<1M
+---
+# NL2Protein Dataset
+## I. Dataset Introduction
+This dataset provides aligned pairs of natural language descriptions and protein
+sequences, where the descriptions integrate protein family information, length
+constraints, and Gene Ontology–based functional relations. The dataset is
+intended for studying natural language–guided protein sequence generation and
+the semantic alignment between textual protein descriptions and sequence space.
+
+The data in this dataset are derived from the UniProt database. Protein
+sequences, organism information, protein family annotations, and associated GO
+terms were downloaded from UniProt and subsequently integrated, filtered, and
+reformatted into a unified text–sequence paired dataset for research use.
+
+Each entry includes:
+- A protein identifier
+- A structured functional description
+- A full-length amino acid sequence
+- The source organism (species)
+- A protein family annotation
+
+The functional description contains:
+- Protein family
+- Protein length range and size category
+- Biological processes
+- Molecular functions
+- Cellular components
+- Parent–child (is_a) relationships between GO terms
+- Cross-ontology relationships, such as:
+  - part_of
+  - occurs_in
+  - regulates / positively_regulates / negatively_regulates
+
+This dataset is designed for natural language–to–protein sequence generation.
+Given a natural language description that specifies functional, and
+biological constraints—such as protein family, length range, Gene Ontology (GO)
+terms from the Biological Process, Molecular Function, and Cellular Component
+namespaces, as well as their parent–child and cross-ontology relationships—the
+task is to directly generate a full-length amino acid sequence that is
+consistent with the provided description. The dataset enables training and
+evaluation of protein language models on text-conditioned sequence generation,
+supporting research in controllable protein design and semantic alignment
+between natural language descriptions and protein sequence space.
+
+## Ⅱ. Data Structure
+Each sample consists of the following fields:
+- ID: Protein identifier (UniProt-style accession)
+- protein: Amino acid sequence
+- Text: Functional description text
+- species: Source organism of the protein (UniProt Organism field)
+- family: Protein family annotation derived from UniProt
+
+| ID | Text | Protein | Species | Family |
+|----|---------|---------|--------|------|
+| A0A017SPL2 | Belongs to the Tryptophan dimethylallyltransferase family.<br>The protein length falls within the range of 301–500 amino acids, belonging to the category of Large proteins.<br>It participates in biological processes such as alkaloid metabolic process.<br>It exhibits molecular functions including prenyltransferase activity. | MQPYHTLSRVLPFPDANQKAWWDKLGPMLLKAMQS<br>QGYDTEAQYAQLGMVYKCVLPYLGEFPTVENDATRWK<br>SFLCPYGIPIEPSLNISQGILRYAFEPIGPDVGTEKDPQN<br>MN | Accumulibacter regalis | Tryptophan dimethylallyltransferase family |
+## Ⅲ. Dataset Loading
+```python
+from datasets import load_dataset
+dataset = load_dataset(
+    "csv",
+    data_files="NL2Protein.csv"
+)
+print(dataset)
+print(dataset["train"][0])
+```
+
+## BibTeX