YTLR

YTLR extracts transcription factor–gene associations from yeast literature to automate identification and extraction of TF binding (TFB) and TF regulatory (TFR) evidence.

Key Features:

• Automated Literature Screening: Automates identification of articles containing TF binding (TFB) and TF regulatory (TFR) evidence.
• TFB article identification accuracy: Identifies articles with TFB evidence with an AUC of 98.8%.
• TF-gene binding extraction accuracy: Extracts detailed TF–gene binding pairs with an AUC of 83.4%.
• TFR article identification accuracy: Identifies articles with TFR evidence with an AUC of 98.2%.
• TF-gene regulatory extraction accuracy: Extracts detailed TF–gene regulatory associations with an AUC of 80.4%.
• Performance versus prior methods: Outperforms previous methods in both identifying relevant literature and extracting TF–gene associations.

Scientific Applications:

• Transcriptional regulation research: Provides high-throughput extraction of TF–gene relations to support studies of yeast transcriptional reprogramming and responses to environmental stress.
• Curatorial pre-screening: Aids manual curation by pre-screening literature for TF binding and regulatory evidence to prioritize curation efforts.

Methodology:

The pipeline identifies articles containing TFB and TFR information, extracts TF–gene binding pairs from TFB-focused articles, and recognizes TF–gene regulatory associations from TFR-focused articles.