ExTRI: Extraction of transcription regulation interactions from literature.The regulation of gene transcription by transcription factors is a fundamental biological process, yet the relations between transcription factors (TF) and their target genes (TG) are still only sparsely covered in databases.  We have generated ExTRI, a knowledge graph of TF-TG relationships, by applying a high recall text-mining pipeline to MedLine abstracts identifying over 100,000 candidate sentences with TF-TG relations.  Our compiled resource encompassing ExTRI together with publicly available resources delivers literature-derived TF-TG interactions for more than 900 of the 1500-1600 proteins considered to function as specific DNA binding TFs. 
ExTRI
We have generated ExTRI, a knowledge graph of TF-TG relationships, by applying a high recall text-mining pipeline to MedLine abstracts identifying over 100,000 candidate sentences with TF-TG relations. 
MedLine abstracts
We have generated ExTRI, a knowledge graph of TF-TG relationships, by applying a high recall text-mining pipeline to MedLine abstracts identifying over 100,000 candidate sentences with TF-TG relations. 
text-mining pipeline
We have generated ExTRI, a knowledge graph of TF-TG relationships, by applying a high recall text-mining pipeline to MedLine abstracts identifying over 100,000 candidate sentences with TF-TG relations.  The obtained result can be used by curators, for network analysis and modelling, for causal reasoning or knowledge graph mining approaches, or serve to benchmark text mining strategies.
knowledge graph
We have generated ExTRI, a knowledge graph of TF-TG relationships, by applying a high recall text-mining pipeline to MedLine abstracts identifying over 100,000 candidate sentences with TF-TG relations.  Validation procedures indicated that about half of the candidate sentences contain true TF-TG relationships.  Post-processing identified 53,000 high confidence sentences containing TF-TG relationships, with a cross-validation F1-score close to 75%.  The resulting collection of TF-TG relationships covers 80% of the relations annotated in existing databases. 
TF-TG relationships